# Directory to use for temporary files storage\r
# REQUIRED - cluster nodes must have access to this directory!\r
# An absolute path is required \r
-cluster.tmp.directory=/homes/pvtroshin/workspace/clustengine/jobsout\r
+cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout\r
\r
# Directory to use for temporary files storage\r
# OPTIONAL defaults to java temporary directory \r
# Relative path within the project will be converted in absolute at runtime\r
-local.tmp.directory=jobsout/local \r
+local.tmp.directory=/cluster/gjb_lab/fc/www-jws/jaba/local_jobsout \r
\r
# Number of threads for tasks execution (valid values between 1 and 2x cpu. \r
# Where x is a number of cores available in the system)\r
# OPTIONAL defaults to the number of cores for core number <=4 and \r
# number of cores-1 for greater core numbers\r
-engine.local.thread.number=3\r
+engine.local.thread.number=2\r
### Clustal configuration ###\r
local.clustalw.bin.windows=binaries/clustalw2.exe\r
local.clustalw.bin=binaries/src/clustalw/src/clustalw2\r
-cluster.clustalw.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/src/clustalw2\r
+cluster.clustalw.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/clustalw/src/clustalw2\r
# Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!\r
# see engine.client.Util.getExecProperty() method for details \r
# So they are case insensitive. \r
local.muscle.bin=binaries/src/muscle/muscle\r
# Beware version of muscle on the cluster older and does not support some \r
# of the newer version attributed thus, will not work with Muscle.java wrapper!\r
-cluster.muscle.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/muscle/muscle\r
+cluster.muscle.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/muscle/muscle\r
#The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored\r
# e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!\r
muscle.-matrix.path=binaries/matrices\r
### Mafft configuration ###\r
#local.mafft.bin.windows=\r
local.mafft.bin=binaries/src/mafft/binaries/mafft\r
-cluster.mafft.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/mafft/core/mafft\r
+cluster.mafft.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/mafft/binaries/mafft\r
mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#/sw/bin/fasta34;\r
mafft.--aamatrix.path=binaries/matrices\r
mafft.presets.file=conf/settings/MafftPresets.xml\r
\r
### Tcoffee configuration ###\r
local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee\r
-cluster.tcoffee.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/tcoffee/t_coffee_source/t_coffee\r
+cluster.tcoffee.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee\r
#/sw/bin/t_coffee\r
# Sub matrix support does not work \r
#tcoffee.-matrix.path=binaries/matrices\r
### Probcons configuration ###\r
#local.probcons.bin.windows=\r
local.probcons.bin=binaries/src/probcons/probcons\r
-cluster.probcons.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/probcons/probcons\r
+cluster.probcons.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/probcons/probcons\r
#Probcons does not support matrix loading - unrecognised option reported! \r
probcons.parameters.file=conf/settings/ProbconsParameters.xml\r
probcons.limits.file=conf/settings/ProbconsLimits.xml\r
\r
# change this \r
-logDir = .\r
+logDir =/homes/www-jws2/logs\r
\r
log4j.rootLogger=ERROR, stdout\r
log4j.appender.stdout=org.apache.log4j.ConsoleAppender\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<limits>\r
- <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
- <limit isDefault="false">\r
- <preset>Disable gap weighting (Speed-oriented)</preset>\r
- <seqNumber>2000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="true">\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>30</seqNumber>\r
- <seqLength>500</seqLength>\r
- </limit>\r
-</limits>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<runnerConfig>\r
- <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
- <options>\r
- <name>NOPGAP</name>\r
- <description>Residue-specific gaps off</description>\r
- <optionNames>-NOPGAP</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html\r
- </furtherDetails>\r
- </options>\r
- <options>\r
- <name>No transition weighting</name>\r
- <description>Disable sequence weighting</description>\r
- <optionNames>-NOWEIGHTS</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html\r
- </furtherDetails>\r
- </options>\r
- <options>\r
- <name>NOHGAP</name>\r
- <description>Hydrophilic gaps off</description>\r
- <optionNames>-NOHGAP</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html\r
- </furtherDetails>\r
- </options>\r
- <prmSeparator>=</prmSeparator>\r
- <parameters>\r
- <name>Transition weighting</name>\r
- <description>Type of the sequence (PROTEIN or DNA)</description>\r
- <optionNames>-TRANSWEIGHT</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html\r
- </furtherDetails>\r
- <defaultValue>0.5</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>0</min>\r
- <max>10</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>Type</name>\r
- <description>Type of the sequence (PROTEIN or DNA)</description>\r
- <optionNames>-TYPE</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html\r
- </furtherDetails>\r
- <defaultValue>PROTEIN</defaultValue>\r
- <possibleValues>PROTEIN</possibleValues>\r
- <possibleValues>DNA</possibleValues>\r
- </parameters>\r
- <parameters>\r
- <name>OUTORDER</name>\r
- <description>As per INPUT or ALIGNED</description>\r
- <optionNames>-OUTORDER</optionNames>\r
- <defaultValue>INPUT</defaultValue>\r
- <possibleValues>INPUT</possibleValues>\r
- <possibleValues>ALIGNED</possibleValues>\r
- </parameters>\r
- <parameters>\r
- <name>MATRIX</name>\r
- <description>Protein weight matrix</description>\r
- <optionNames>-MATRIX</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html\r
- </furtherDetails>\r
- <defaultValue>BLOSUM62</defaultValue>\r
- <!-- Clustal build in matrices\r
- <possibleValues>BLOSUM</possibleValues>\r
- <possibleValues>PAM</possibleValues>\r
- <possibleValues>ID</possibleValues>\r
- <possibleValues>GONNET</possibleValues>\r
- -->\r
- <possibleValues>BLOSUM100</possibleValues>\r
- <possibleValues>BLOSUM30</possibleValues>\r
- <possibleValues>BLOSUM35</possibleValues>\r
- <possibleValues>BLOSUM40</possibleValues>\r
- <possibleValues>BLOSUM45</possibleValues>\r
- <possibleValues>BLOSUM50</possibleValues>\r
- <possibleValues>BLOSUM55</possibleValues>\r
- <possibleValues>BLOSUM60</possibleValues>\r
- <possibleValues>BLOSUM62</possibleValues>\r
- <possibleValues>BLOSUM65</possibleValues>\r
- <possibleValues>BLOSUM70</possibleValues>\r
- <possibleValues>BLOSUM75</possibleValues>\r
- <possibleValues>BLOSUM80</possibleValues>\r
- <possibleValues>BLOSUM85</possibleValues>\r
- <possibleValues>BLOSUM90</possibleValues>\r
- <possibleValues>BLOSUMN</possibleValues>\r
- <possibleValues>DAYHOFF</possibleValues>\r
- <possibleValues>GONNET</possibleValues>\r
- <possibleValues>IDENTITY</possibleValues>\r
- <possibleValues>MATCH</possibleValues>\r
- <possibleValues>NUC.4.2</possibleValues>\r
- <possibleValues>NUC.4.4</possibleValues>\r
- <possibleValues>PAM10</possibleValues>\r
- <possibleValues>PAM100</possibleValues>\r
- <possibleValues>PAM110</possibleValues>\r
- <possibleValues>PAM120</possibleValues>\r
- <possibleValues>PAM130</possibleValues>\r
- <possibleValues>PAM140</possibleValues>\r
- <possibleValues>PAM150</possibleValues>\r
- <possibleValues>PAM160</possibleValues>\r
- <possibleValues>PAM170</possibleValues>\r
- <possibleValues>PAM180</possibleValues>\r
- <possibleValues>PAM190</possibleValues>\r
- <possibleValues>PAM20</possibleValues>\r
- <possibleValues>PAM200</possibleValues>\r
- <possibleValues>PAM210</possibleValues>\r
- <possibleValues>PAM220</possibleValues>\r
- <possibleValues>PAM230</possibleValues>\r
- <possibleValues>PAM240</possibleValues>\r
- <possibleValues>PAM250</possibleValues>\r
- <possibleValues>PAM260</possibleValues>\r
- <possibleValues>PAM270</possibleValues>\r
- <possibleValues>PAM280</possibleValues>\r
- <possibleValues>PAM290</possibleValues>\r
- <possibleValues>PAM30</possibleValues>\r
- <possibleValues>PAM300</possibleValues>\r
- <possibleValues>PAM310</possibleValues>\r
- <possibleValues>PAM320</possibleValues>\r
- <possibleValues>PAM330</possibleValues>\r
- <possibleValues>PAM340</possibleValues>\r
- <possibleValues>PAM350</possibleValues>\r
- <possibleValues>PAM360</possibleValues>\r
- <possibleValues>PAM370</possibleValues>\r
- <possibleValues>PAM380</possibleValues>\r
- <possibleValues>PAM390</possibleValues>\r
- <possibleValues>PAM40</possibleValues>\r
- <possibleValues>PAM400</possibleValues>\r
- <possibleValues>PAM410</possibleValues>\r
- <possibleValues>PAM420</possibleValues>\r
- <possibleValues>PAM430</possibleValues>\r
- <possibleValues>PAM440</possibleValues>\r
- <possibleValues>PAM450</possibleValues>\r
- <possibleValues>PAM460</possibleValues>\r
- <possibleValues>PAM470</possibleValues>\r
- <possibleValues>PAM480</possibleValues>\r
- <possibleValues>PAM490</possibleValues>\r
- <possibleValues>PAM50</possibleValues>\r
- <possibleValues>PAM500</possibleValues>\r
- <possibleValues>PAM60</possibleValues>\r
- <possibleValues>PAM70</possibleValues>\r
- <possibleValues>PAM80</possibleValues>\r
- <possibleValues>PAM90</possibleValues>\r
- </parameters>\r
- <parameters>\r
- <name>GAPOPEN</name>\r
- <description>Gap opening penalty</description>\r
- <optionNames>-GAPOPEN</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html\r
- </furtherDetails>\r
- <defaultValue>10</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>0</min>\r
- <max>1000</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>-GAPEXT</name>\r
- <description>Gap extension penalty</description>\r
- <optionNames>-GAPEXT</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html\r
- </furtherDetails>\r
- <defaultValue>0.1</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>0</min>\r
- <max>10</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>ENDGAPS</name>\r
- <description>End gap separation pen</description>\r
- <optionNames>-ENDGAPS</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html\r
- </furtherDetails>\r
- <defaultValue>0.5</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>0</min>\r
- <max>10</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>GAPDIST</name>\r
- <description>Gap separation pen. range</description>\r
- <optionNames>-GAPDIST</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html\r
- </furtherDetails>\r
- <defaultValue>1</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>0</min>\r
- <max>50</max>\r
- </validValue>\r
- </parameters>\r
-</runnerConfig>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<presets>\r
- <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
- <preset>\r
- <name>Disable gap weighting (Speed-oriented)</name>\r
- <description></description>\r
- <optlist>\r
- <option>-NOPGAP</option>\r
- <option>-NOWEIGHTS</option>\r
- <option>-NOHGAP</option>\r
- </optlist>\r
- </preset>\r
-</presets>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<limits>\r
- <runnerClassName>compbio.runner.mafft.Mafft</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>30</seqNumber>\r
- <seqLength>500</seqLength>\r
- </limit>\r
-</limits>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes" ?>\r
-<runnerConfig >\r
- <runnerClassName>compbio.runner.mafft.Mafft</runnerClassName>\r
- <options isRequired="false">\r
- <name>Shared 6mers distance calculation</name>\r
- <description>Distance is calculated based on the number of shared 6mers. Default: on</description>\r
- <optionNames>--6merpair</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>--6merpair</defaultValue>\r
- </options>\r
- <options isRequired="true">\r
- <name>Output sequences order</name>\r
- <description>--inputorder - Output order: same as input. \r
- --reorder - Output order: aligned. Default: same as input</description>\r
- <optionNames>--inputorder</optionNames>\r
- <optionNames>--reorder</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>--inputorder</defaultValue>\r
- </options>\r
- <options isRequired="false">\r
- <name>Sequence type</name>\r
- <description>\r
- --nuc - Assume the sequences are nucleotide.\r
- --amino - Assume the sequences are amino acid. </description>\r
- <optionNames>--amino</optionNames>\r
- <optionNames>--nuc</optionNames>\r
- <optionNames>--auto</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>--auto</defaultValue>\r
- </options>\r
- <options isRequired="false">\r
- <name>Pairwise alignment computation method</name>\r
- <description>\r
- --globalpair\r
- All pairwise alignments are computed with the Needleman-Wunsch algorithm. More accurate but slower than --6merpair. Suitable for a set of globally alignable sequences. Applicable to up to ~200 sequences. A combination with --maxiterate 1000 is recommended (G-INS-i). Default: off (6mer distance is used)\r
- --genafpair \r
- All pairwise alignments are computed with a local algorithm with the generalized affine gap cost (Altschul 1998). More accurate but slower than --6merpair. Suitable when large internal gaps are expected. Applicable to up to ~200 sequences. A combination with --maxiterate 1000 is recommended (E-INS-i). Default: off (6mer distance is used)\r
- --fastapair\r
- All pairwise alignments are computed with FASTA (Pearson and Lipman 1988). FASTA is required. Default: off (6mer distance is used)\r
- --localpair\r
- All pairwise alignments are computed with the Smith-Waterman algorithm. More accurate but slower than --6merpair. Suitable for a set of locally alignable sequences. Applicable to up to ~200 sequences. A combination with --maxiterate 1000 is recommended (L-INS-i). Default: off (6mer distance is used)\r
- </description>\r
- <optionNames>--fastapair</optionNames>\r
- <optionNames>--genafpair</optionNames>\r
- <optionNames>--localpair</optionNames>\r
- <optionNames>--globalpair</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>--localpair</defaultValue>\r
- </options>\r
- <options isRequired="false">\r
- <name>FFT approximation</name>\r
- <description>Use / Do not use FFT approximation in group-to-group alignment. Default: off</description>\r
- <optionNames>--nofft</optionNames>\r
- <optionNames>--fft</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>--nofft</defaultValue>\r
- </options>\r
- <options isRequired="false">\r
- <name>No score</name>\r
- <description>Alignment score is not checked in the iterative refinement stage. Default: off (score is checked)</description>\r
- <optionNames>--noscore</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- </options>\r
- <options isRequired="false">\r
- <name>Part tree</name>\r
- <description>\r
- --parttree - Use a fast tree-building method (PartTree, Katoh and Toh 2007) with the 6mer distance. \r
- --dpparttree - the PartTree algorithm is used with distances based on DP. \r
- Slightly more accurate and slower than --parttree. \r
- --fastaparttree - The PartTree algorithm is used with distances based on FASTA. \r
- Slightly more accurate and slower than --parttree. \r
- All methods recommended for a large number (> ~10,000) of sequences are input.\r
- </description> \r
- <optionNames>--dpparttree</optionNames>\r
- <optionNames>--parttree</optionNames>\r
- <optionNames>--fastaparttree</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>--fastaparttree</defaultValue>\r
- </options>\r
- <prmSeparator> </prmSeparator>\r
- <parameters isRequired="false">\r
- <name>Max iteration number</name>\r
- <description>number cycles of iterative refinement are performed. Default: 0</description>\r
- <optionNames>--maxiterate</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>0</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>0</min>\r
- <max>1000</max>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Partsize</name>\r
- <description>The number of partitions in the PartTree algorithm. Default: 50</description>\r
- <optionNames>--partsize</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>50</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>1</min>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Group size</name>\r
- <description>Do not make alignment larger than number sequences. Valid only with the --*parttree options. Default: the number of input sequences</description>\r
- <optionNames>--groupsize</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>20</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>0</min>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Guide tree rebuild</name>\r
- <description>Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2</description>\r
- <optionNames>--retree</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>2</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>1</min>\r
- <max>100</max>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Gap opening penalty</name>\r
- <description>Gap opening penalty at group-to-group alignment. Default: 1.53</description>\r
- <optionNames>--op</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>1.53</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>0</min>\r
- </validValue>\r
- </parameters> \r
- <parameters isRequired="false">\r
- <name>Group-to-group gap extension penalty</name>\r
- <description>Offset value, which works like gap extension penalty, for group-to-group alignment. Deafult: 0.123</description>\r
- <optionNames>--ep</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>0.123</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>0</min>\r
- </validValue>\r
- </parameters> \r
- <parameters isRequired="false">\r
- <name>Gap opening penalty at local pairwise alignment</name>\r
- <description>Gap opening penalty at local pairwise alignment. Valid when the --localpair or --genafpair option is selected. Default: -2.00</description>\r
- <optionNames>--lop</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>-2.00</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <max>0</max>\r
- </validValue>\r
- </parameters> \r
- <parameters isRequired="false">\r
- <name>Matrix</name>\r
- <description>Substitution Matrix to use</description>\r
- <optionNames>--aamatrix</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>BLOSUM62</defaultValue>\r
- <possibleValues>BLOSUM100</possibleValues>\r
- <possibleValues>BLOSUM30</possibleValues>\r
- <possibleValues>BLOSUM35</possibleValues>\r
- <possibleValues>BLOSUM40</possibleValues>\r
- <possibleValues>BLOSUM45</possibleValues>\r
- <possibleValues>BLOSUM50</possibleValues>\r
- <possibleValues>BLOSUM55</possibleValues>\r
- <possibleValues>BLOSUM60</possibleValues>\r
- <possibleValues>BLOSUM62</possibleValues>\r
- <possibleValues>BLOSUM65</possibleValues>\r
- <possibleValues>BLOSUM70</possibleValues>\r
- <possibleValues>BLOSUM75</possibleValues>\r
- <possibleValues>BLOSUM80</possibleValues>\r
- <possibleValues>BLOSUM85</possibleValues>\r
- <possibleValues>BLOSUM90</possibleValues>\r
- <possibleValues>BLOSUMN</possibleValues>\r
- <possibleValues>DAYHOFF</possibleValues>\r
- <possibleValues>GONNET</possibleValues>\r
- <possibleValues>IDENTITY</possibleValues>\r
- <possibleValues>MATCH</possibleValues>\r
- <possibleValues>PAM10</possibleValues>\r
- <possibleValues>PAM100</possibleValues>\r
- <possibleValues>PAM110</possibleValues>\r
- <possibleValues>PAM120</possibleValues>\r
- <possibleValues>PAM130</possibleValues>\r
- <possibleValues>PAM140</possibleValues>\r
- <possibleValues>PAM150</possibleValues>\r
- <possibleValues>PAM160</possibleValues>\r
- <possibleValues>PAM170</possibleValues>\r
- <possibleValues>PAM180</possibleValues>\r
- <possibleValues>PAM190</possibleValues>\r
- <possibleValues>PAM20</possibleValues>\r
- <possibleValues>PAM200</possibleValues>\r
- <possibleValues>PAM210</possibleValues>\r
- <possibleValues>PAM220</possibleValues>\r
- <possibleValues>PAM230</possibleValues>\r
- <possibleValues>PAM240</possibleValues>\r
- <possibleValues>PAM250</possibleValues>\r
- <possibleValues>PAM260</possibleValues>\r
- <possibleValues>PAM270</possibleValues>\r
- <possibleValues>PAM280</possibleValues>\r
- <possibleValues>PAM290</possibleValues>\r
- <possibleValues>PAM30</possibleValues>\r
- <possibleValues>PAM300</possibleValues>\r
- <possibleValues>PAM310</possibleValues>\r
- <possibleValues>PAM320</possibleValues>\r
- <possibleValues>PAM330</possibleValues>\r
- <possibleValues>PAM340</possibleValues>\r
- <possibleValues>PAM350</possibleValues>\r
- <possibleValues>PAM360</possibleValues>\r
- <possibleValues>PAM370</possibleValues>\r
- <possibleValues>PAM380</possibleValues>\r
- <possibleValues>PAM390</possibleValues>\r
- <possibleValues>PAM40</possibleValues>\r
- <possibleValues>PAM400</possibleValues>\r
- <possibleValues>PAM410</possibleValues>\r
- <possibleValues>PAM420</possibleValues>\r
- <possibleValues>PAM430</possibleValues>\r
- <possibleValues>PAM440</possibleValues>\r
- <possibleValues>PAM450</possibleValues>\r
- <possibleValues>PAM460</possibleValues>\r
- <possibleValues>PAM470</possibleValues>\r
- <possibleValues>PAM480</possibleValues>\r
- <possibleValues>PAM490</possibleValues>\r
- <possibleValues>PAM50</possibleValues>\r
- <possibleValues>PAM500</possibleValues>\r
- <possibleValues>PAM60</possibleValues>\r
- <possibleValues>PAM70</possibleValues>\r
- <possibleValues>PAM80</possibleValues>\r
- <possibleValues>PAM90</possibleValues>\r
- </parameters>\r
-</runnerConfig>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<presets>\r
- <runnerClassName>compbio.runner.mafft.Mafft</runnerClassName>\r
- <preset>\r
- <name>L-INS-i (Accuracy-oriented)</name>\r
- <description>L-INS-i (probably most accurate; recommended for <200\r
- sequences; iterative refinement method incorporating local pairwise\r
- alignment information)</description>\r
- <optlist>\r
- <option>--localpair</option>\r
- <option>--maxiterate 1000</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>G-INS-i (Accuracy-oriented)</name>\r
- <description>G-INS-i (suitable for sequences of similar lengths;\r
- recommended for <200 sequences; iterative refinement method\r
- incorporating global pairwise alignment information)</description>\r
- <optlist>\r
- <option>--globalpair</option>\r
- <option>--maxiterate 1000</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>E-INS-i (Accuracy-oriented)</name>\r
- <description>E-INS-i (suitable for sequences containing large\r
- unalignable regions; recommended for <200 sequences)</description>\r
- <optlist>\r
- <option>--ep 0</option>\r
- <option>--genafpair</option>\r
- <option>--maxiterate 1000</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>FFT-NS-i (Speed oriented)</name>\r
- <description>FFT-NS-i (iterative refinement method; two cycles only)</description>\r
- <optlist>\r
- <option>--retree 2</option>\r
- <option>--maxiterate 2</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>FFT-NS-1 (Speed oriented)</name>\r
- <description>FFT-NS-1 (very fast; recommended for >2000 sequences;\r
- progressive method with a rough guide tree)</description>\r
- <optlist>\r
- <option>--retree 1</option>\r
- <option>--maxiterate 0</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>NW-NS-PartTree-1 (Speed oriented)</name>\r
- <description>NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000\r
- sequences; progressive method with the PartTree algorithm)</description>\r
- <optlist>\r
- <option>--retree 1</option>\r
- <option>--maxiterate 0</option>\r
- <option>--nofft</option>\r
- <option>--parttree</option>\r
- </optlist>\r
- </preset>\r
-</presets>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<limits>\r
- <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>30</seqNumber>\r
- <seqLength>500</seqLength>\r
- </limit>\r
-</limits>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<runnerConfig>\r
- <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
- <options isRequired="false">\r
- <name>Group sequences</name>\r
- <description>Group sequences by similarity (this is the default) or preserve the input order</description>\r
- <optionNames>-group</optionNames>\r
- <optionNames>-stable</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>-stable</defaultValue>\r
- </options>\r
- <options isRequired="false">\r
- <name>Anchor optimisation</name>\r
- <description>Enable/disable anchor optimization in tree dependent refinement iterations</description>\r
- <optionNames>-anchors</optionNames>\r
- <optionNames>-noanchors</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>-anchors</defaultValue>\r
- </options>\r
- <options isRequired="false">\r
- <name>Root alignment computation method</name>\r
- <description>Use Steven Brenner's method for computing the root alignment.</description>\r
- <optionNames>-brenner</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- </options>\r
- <!-- This option make sense only in conjunction with -tree which we do not currently support\r
- <options isRequired="false">\r
- <name>Fast clustering of input sequences</name>\r
- <description>Perform fast clustering of input sequences.</description>\r
- <optionNames>-cluster</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- </options>\r
- -->\r
- <options isRequired="false">\r
- <name>dimer</name>\r
- <description>Use dimer approximation for the SP score (faster, slightly less accurate)</description>\r
- <optionNames>-dimer</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- </options>\r
- <options isRequired="false">\r
- <name>Diagonal</name>\r
- <description>Use diagonal optimizations. Faster, especially for closely related sequences, but may be less accurate.</description>\r
- <optionNames>-diags</optionNames>\r
- </options>\r
- <options isRequired="false">\r
- <name>Diagonal 1</name>\r
- <description>Use diagonal optimizations in first iteration (faster for similar sequences)</description>\r
- <optionNames>-diags1</optionNames>\r
- </options>\r
- <options isRequired="false">\r
- <name>Profile scoring method</name>\r
- <description>le - use log-expectation profile score VTML240 (default for amino acid sequences.)\r
- sp - use sum-of-pairs protein profile score (PAM200).\r
- sv - use sum-of-pairs profile score (VTML240)</description>\r
- <optionNames>-le</optionNames>\r
- <optionNames>-sp</optionNames>\r
- <optionNames>-sv</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>-le</defaultValue>\r
- </options>\r
- <prmSeparator> </prmSeparator>\r
- <parameters isRequired="false">\r
- <name>Sequence type</name>\r
- <description>Sequence type - Amino acid/Nucleotide </description>\r
- <optionNames>-seqtype</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>auto</defaultValue>\r
- <possibleValues>auto</possibleValues>\r
- <possibleValues>protein</possibleValues>\r
- <possibleValues>nucleo</possibleValues>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Maxiters</name>\r
- <description>Maximum number of iterations (integer, default 16)</description>\r
- <optionNames>-maxiters</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>16</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>1</min>\r
- <max>100</max>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Matrix</name>\r
- <description>Substitution Matrix to use</description>\r
- <optionNames>-matrix</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>BLOSUM62</defaultValue>\r
- <possibleValues>BLOSUM100</possibleValues>\r
- <possibleValues>BLOSUM30</possibleValues>\r
- <possibleValues>BLOSUM35</possibleValues>\r
- <possibleValues>BLOSUM40</possibleValues>\r
- <possibleValues>BLOSUM45</possibleValues>\r
- <possibleValues>BLOSUM50</possibleValues>\r
- <possibleValues>BLOSUM55</possibleValues>\r
- <possibleValues>BLOSUM60</possibleValues>\r
- <possibleValues>BLOSUM62</possibleValues>\r
- <possibleValues>BLOSUM65</possibleValues>\r
- <possibleValues>BLOSUM70</possibleValues>\r
- <possibleValues>BLOSUM75</possibleValues>\r
- <possibleValues>BLOSUM80</possibleValues>\r
- <possibleValues>BLOSUM85</possibleValues>\r
- <possibleValues>BLOSUM90</possibleValues>\r
- <possibleValues>BLOSUMN</possibleValues>\r
- <possibleValues>DAYHOFF</possibleValues>\r
- <possibleValues>GONNET</possibleValues>\r
- <possibleValues>IDENTITY</possibleValues>\r
- <possibleValues>MATCH</possibleValues>\r
- <possibleValues>NUC.4.2</possibleValues>\r
- <possibleValues>NUC.4.4</possibleValues>\r
- <possibleValues>PAM10</possibleValues>\r
- <possibleValues>PAM100</possibleValues>\r
- <possibleValues>PAM110</possibleValues>\r
- <possibleValues>PAM120</possibleValues>\r
- <possibleValues>PAM130</possibleValues>\r
- <possibleValues>PAM140</possibleValues>\r
- <possibleValues>PAM150</possibleValues>\r
- <possibleValues>PAM160</possibleValues>\r
- <possibleValues>PAM170</possibleValues>\r
- <possibleValues>PAM180</possibleValues>\r
- <possibleValues>PAM190</possibleValues>\r
- <possibleValues>PAM20</possibleValues>\r
- <possibleValues>PAM200</possibleValues>\r
- <possibleValues>PAM210</possibleValues>\r
- <possibleValues>PAM220</possibleValues>\r
- <possibleValues>PAM230</possibleValues>\r
- <possibleValues>PAM240</possibleValues>\r
- <possibleValues>PAM250</possibleValues>\r
- <possibleValues>PAM260</possibleValues>\r
- <possibleValues>PAM270</possibleValues>\r
- <possibleValues>PAM280</possibleValues>\r
- <possibleValues>PAM290</possibleValues>\r
- <possibleValues>PAM30</possibleValues>\r
- <possibleValues>PAM300</possibleValues>\r
- <possibleValues>PAM310</possibleValues>\r
- <possibleValues>PAM320</possibleValues>\r
- <possibleValues>PAM330</possibleValues>\r
- <possibleValues>PAM340</possibleValues>\r
- <possibleValues>PAM350</possibleValues>\r
- <possibleValues>PAM360</possibleValues>\r
- <possibleValues>PAM370</possibleValues>\r
- <possibleValues>PAM380</possibleValues>\r
- <possibleValues>PAM390</possibleValues>\r
- <possibleValues>PAM40</possibleValues>\r
- <possibleValues>PAM400</possibleValues>\r
- <possibleValues>PAM410</possibleValues>\r
- <possibleValues>PAM420</possibleValues>\r
- <possibleValues>PAM430</possibleValues>\r
- <possibleValues>PAM440</possibleValues>\r
- <possibleValues>PAM450</possibleValues>\r
- <possibleValues>PAM460</possibleValues>\r
- <possibleValues>PAM470</possibleValues>\r
- <possibleValues>PAM480</possibleValues>\r
- <possibleValues>PAM490</possibleValues>\r
- <possibleValues>PAM50</possibleValues>\r
- <possibleValues>PAM500</possibleValues>\r
- <possibleValues>PAM60</possibleValues>\r
- <possibleValues>PAM70</possibleValues>\r
- <possibleValues>PAM80</possibleValues>\r
- <possibleValues>PAM90</possibleValues>\r
- </parameters>\r
- <parameters>\r
- <name>Gap open penalty</name>\r
- <description>Gap opening penalty. Must be negative</description>\r
- <optionNames>-gapopen</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>-12.0</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>-100</min>\r
- <max>0</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>Gap extension penalty</name>\r
- <description>Gap extension penalty. Must be negative</description>\r
- <optionNames>-gapextend</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>-1.0</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>-100</min>\r
- <max>0</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>Center</name>\r
- <description>Center parameter. Should be negative.</description>\r
- <optionNames>-center</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>0.0</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>-100</min>\r
- <max>0</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>Hydro</name>\r
- <description>Window size for determining whether a region is hydrophobic.</description>\r
- <optionNames>-hydro</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>5</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>0</min>\r
- <max>100</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>Hydrofactor</name>\r
- <description>Multiplier for gap open/close penalties in hydrophobic regions.</description>\r
- <optionNames>-hydrofactor</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>1.2</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>0</min>\r
- <max>10</max>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>cluster1</name>\r
- <description>Clustering method to use on the iteration 1</description>\r
- <optionNames>-cluster1</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>upgma</defaultValue>\r
- <possibleValues>upgma</possibleValues>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>cluster2</name>\r
- <description>Clustering method to use on the iteration 2 and all subsequent itarations</description>\r
- <optionNames>-cluster2</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>upgmb</defaultValue>\r
- <possibleValues>upgmb</possibleValues>\r
- <possibleValues>neighborjoining</possibleValues>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Sequence weighting scheme 1</name>\r
- <description>Sequence weighting scheme to use on the iteration 1 and 2 \r
- none=all sequences have equal weight.\r
- henikoff=Henikoff & Henikoff weighting scheme.\r
- henikoffpb=Modified Henikoff scheme as used in PSI-BLAST.\r
- clustalw=CLUSTALW method.\r
- threeway=Gotoh three-way method</description>\r
- <optionNames>-weight1</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>clustalw</defaultValue>\r
- <possibleValues>none</possibleValues>\r
- <possibleValues>henikoff</possibleValues>\r
- <possibleValues>henikoffpb</possibleValues>\r
- <possibleValues>gsc</possibleValues>\r
- <possibleValues>clustalw</possibleValues>\r
- <possibleValues>threeway</possibleValues>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Sequence weighting scheme 2</name>\r
- <description>Sequence weighting scheme to use on the iteration 3 and all subsequent \r
- iterations for tree-dependent refinement.\r
- none=all sequences have equal weight.\r
- henikoff=Henikoff & Henikoff weighting scheme.\r
- henikoffpb=Modified Henikoff scheme as used in PSI-BLAST.\r
- clustalw=CLUSTALW method.\r
- threeway=Gotoh three-way method</description>\r
- <optionNames>-weight2</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>clustalw</defaultValue>\r
- <possibleValues>none</possibleValues>\r
- <possibleValues>henikoff</possibleValues>\r
- <possibleValues>henikoffpb</possibleValues>\r
- <possibleValues>gsc</possibleValues>\r
- <possibleValues>clustalw</possibleValues>\r
- <possibleValues>threeway</possibleValues>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Distance1</name>\r
- <description>Distance measure for iteration 1. Defaults Kmer6_6 (for amino ) or Kmer4_6 (for nucleo)</description>\r
- <optionNames>-distance1</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>kmer6_6</defaultValue>\r
- <possibleValues>kmer6_6</possibleValues>\r
- <possibleValues>kmer20_3</possibleValues>\r
- <possibleValues>kbit20_3</possibleValues>\r
- <possibleValues>kmer20_4</possibleValues>\r
- <possibleValues>kmer4_6</possibleValues>\r
- </parameters>\r
-</runnerConfig>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<presets>\r
- <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
- <preset>\r
- <name>Protein alignment(Fastest speed)</name>\r
- <description>Fastest possible speed for protein sequences. Gives acceptable quality alignments for closely related sequences</description>\r
- <optlist>\r
- <option>-maxiters 1</option>\r
- <option>-diags</option>\r
- <option>-sv</option>\r
- <option>-distance1 kbit20_3</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>Nucleotide alignment(Fastest speed)</name>\r
- <description>Fastest possible speed for nucleotide sequences. Gives acceptable quality alignments for closely related sequences</description>\r
- <optlist>\r
- <option>-maxiters 1</option>\r
- <option>-diags</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>Huge alignments (speed-oriented)</name>\r
- <description>Very large number of sequences (several thousand), or they are very long, </description>\r
- <optlist>\r
- <option>-maxiters 1</option>\r
- <option>-diags1</option>\r
- <option>-sv</option>\r
- </optlist>\r
- </preset>\r
-</presets>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<limits>\r
- <runnerClassName>compbio.runner.probcons.Probcons</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>30</seqNumber>\r
- <seqLength>500</seqLength>\r
- </limit>\r
-</limits>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<runnerConfig>\r
- <runnerClassName>compbio.runner.probcons.Probcons</runnerClassName>\r
- <!-- This is requires training -t, but training output probabil file instead of the alignment \r
- <options>\r
- <name>Reestimate EP</name>\r
- <description>Reestimate emission probabilities.</description>\r
- <optionNames>-e</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- </options>\r
- -->\r
- <options>\r
- <name>Output aligned</name>\r
- <description>Output sequences in alignment order rather than input order</description>\r
- <optionNames>-a</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- </options>\r
- <prmSeparator> </prmSeparator>\r
- <!-- unsupported in practice \r
- <parameters>\r
- <name>MATRIX</name>\r
- <description>Protein weight matrix. Specifies the emission probabilities that are to be used for scoring alignments.</description>\r
- <optionNames>-m</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>BLOSUM62</defaultValue>\r
- <possibleValues>BLOSUM100</possibleValues>\r
- <possibleValues>BLOSUM30</possibleValues>\r
- <possibleValues>BLOSUM35</possibleValues>\r
- <possibleValues>BLOSUM40</possibleValues>\r
- <possibleValues>BLOSUM45</possibleValues>\r
- <possibleValues>BLOSUM50</possibleValues>\r
- <possibleValues>BLOSUM55</possibleValues>\r
- <possibleValues>BLOSUM60</possibleValues>\r
- <possibleValues>BLOSUM62</possibleValues>\r
- <possibleValues>BLOSUM65</possibleValues>\r
- <possibleValues>BLOSUM70</possibleValues>\r
- <possibleValues>BLOSUM75</possibleValues>\r
- <possibleValues>BLOSUM80</possibleValues>\r
- <possibleValues>BLOSUM85</possibleValues>\r
- <possibleValues>BLOSUM90</possibleValues>\r
- <possibleValues>BLOSUMN</possibleValues>\r
- <possibleValues>DAYHOFF</possibleValues>\r
- <possibleValues>GONNET</possibleValues>\r
- <possibleValues>IDENTITY</possibleValues>\r
- <possibleValues>MATCH</possibleValues>\r
- <possibleValues>NUC.4.2</possibleValues>\r
- <possibleValues>NUC.4.4</possibleValues>\r
- <possibleValues>PAM10</possibleValues>\r
- <possibleValues>PAM100</possibleValues>\r
- <possibleValues>PAM110</possibleValues>\r
- <possibleValues>PAM120</possibleValues>\r
- <possibleValues>PAM130</possibleValues>\r
- <possibleValues>PAM140</possibleValues>\r
- <possibleValues>PAM150</possibleValues>\r
- <possibleValues>PAM160</possibleValues>\r
- <possibleValues>PAM170</possibleValues>\r
- <possibleValues>PAM180</possibleValues>\r
- <possibleValues>PAM190</possibleValues>\r
- <possibleValues>PAM20</possibleValues>\r
- <possibleValues>PAM200</possibleValues>\r
- <possibleValues>PAM210</possibleValues>\r
- <possibleValues>PAM220</possibleValues>\r
- <possibleValues>PAM230</possibleValues>\r
- <possibleValues>PAM240</possibleValues>\r
- <possibleValues>PAM250</possibleValues>\r
- <possibleValues>PAM260</possibleValues>\r
- <possibleValues>PAM270</possibleValues>\r
- <possibleValues>PAM280</possibleValues>\r
- <possibleValues>PAM290</possibleValues>\r
- <possibleValues>PAM30</possibleValues>\r
- <possibleValues>PAM300</possibleValues>\r
- <possibleValues>PAM310</possibleValues>\r
- <possibleValues>PAM320</possibleValues>\r
- <possibleValues>PAM330</possibleValues>\r
- <possibleValues>PAM340</possibleValues>\r
- <possibleValues>PAM350</possibleValues>\r
- <possibleValues>PAM360</possibleValues>\r
- <possibleValues>PAM370</possibleValues>\r
- <possibleValues>PAM380</possibleValues>\r
- <possibleValues>PAM390</possibleValues>\r
- <possibleValues>PAM40</possibleValues>\r
- <possibleValues>PAM400</possibleValues>\r
- <possibleValues>PAM410</possibleValues>\r
- <possibleValues>PAM420</possibleValues>\r
- <possibleValues>PAM430</possibleValues>\r
- <possibleValues>PAM440</possibleValues>\r
- <possibleValues>PAM450</possibleValues>\r
- <possibleValues>PAM460</possibleValues>\r
- <possibleValues>PAM470</possibleValues>\r
- <possibleValues>PAM480</possibleValues>\r
- <possibleValues>PAM490</possibleValues>\r
- <possibleValues>PAM50</possibleValues>\r
- <possibleValues>PAM500</possibleValues>\r
- <possibleValues>PAM60</possibleValues>\r
- <possibleValues>PAM70</possibleValues>\r
- <possibleValues>PAM80</possibleValues>\r
- <possibleValues>PAM90</possibleValues>\r
- </parameters>\r
- -->\r
- <parameters>\r
- <name>Rounds of pre-training before aligning the sequences</name>\r
- <description>This specifies the number of rounds of EM to be applied on the set of sequences being\r
-aligned. This option is used in case the default parameters are not appropriate for the\r
-particular sequences being aligned; in general, this option is not recommended as it may\r
-lead to unstable alignment parameters.</description>\r
- <optionNames>-pre</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>0</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>0</min>\r
- <max>20</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>Passes of iterative refinement</name>\r
- <description>This specifies the number of iterations of iterative refinement to be performed. In each\r
-stage of iterative refinement, the set of sequences in the alignment is randomly\r
-partitioned into two groups. After projecting the alignments to these groups, the two\r
-groups are realigned, resulting in an alignment whose objective score is guaranteed to be\r
-at least that of the original alignment</description>\r
- <optionNames>-ir</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>100</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>0</min>\r
- <max>1000</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>Passes of consistency transformation</name>\r
- <description>Each pass applies one round of the consistency transformation on the set of sequences.\r
- The consistency transformation is described in detail in the mentioned papers. In each\r
- round, the aligner computes the consistency transformation for each pair of sequences\r
- using all other sequences. The aligner then updates the posterior probability matrices of\r
- the pairwise alignments.</description>\r
- <optionNames>-c</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>2</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>0</min>\r
- <max>5</max>\r
- </validValue>\r
- </parameters>\r
-</runnerConfig>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<limits>\r
- <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>30</seqNumber>\r
- <seqLength>500</seqLength>\r
- </limit>\r
-</limits>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<runnerConfig>\r
- <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
- <options isRequired="false">\r
- <name>Search sequences in PDB</name>\r
- <description>\r
- Forces t_coffee to run extract_from_pdb to check the pdb status of each sequence. \r
- This can considerably slow down the program. \r
- </description>\r
- <optionNames>-check_pdb_status</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- </options>\r
- <prmSeparator>=</prmSeparator>\r
- <!-- ERROR: When using -evaluate, Provide a multiple sequence alignment via the -infile flag [FATAL:T-COFFEE] \r
- mcoffee: compares alignmens obtained by different programmes\r
- -->\r
- <parameters isRequired="false">\r
- <name>Preset Mode</name>\r
- <description>It indicates that t_coffee will use some hard coded parameters. These include:\r
- quickaln: Very fast, sequence type - all, accuracy - medium low \r
- </description>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <optionNames>-mode</optionNames>\r
- <defaultValue>quickaln</defaultValue>\r
- <possibleValues>quickaln</possibleValues>\r
- </parameters>\r
- <!--\r
- All the options below need proper installation!\r
- rcoffee does not work as it fails to find the "templates" \r
- <description>\r
- This require blast to be setup properly see also Presets\r
- dali: a mode used to combine dali pairwise alignments\r
- 3dcoffee: runs t_coffee with the 3dcoffee parameterization\r
- accurate: slow, sequence type - protein, accuracy - high\r
- expresso: slow, sequence type - all, accuracy - high\r
- rcoffee: slow, sequence type - RNA, accuracy - high\r
- </description>\r
- <possibleValues>expresso</possibleValues>\r
- <possibleValues>dali</possibleValues>\r
- <possibleValues>3dcoffee</possibleValues>\r
- <possibleValues>accurate</possibleValues>\r
- <possibleValues>rcoffee</possibleValues>\r
- -->\r
-<!-- Parameter with textual value \r
- <parameters isRequired="false">\r
- <name>Structures</name>\r
- <description>Reads or fetch a pdb file. Please enter up to 200 pdb identifiers </description>\r
- <optionNames>-pdb</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- </parameters>\r
- -->\r
- <parameters isRequired="false">\r
- <name>Distance matrix computation method</name>\r
- <description>\r
- This flag indicates the method used for computing the distance matrix (distance between every pair of sequences) required for the computation of the dendrogram. \r
- Slow The chosen dp_mode using the extended library, \r
- fast: The fasta dp_mode using the extended library.\r
- very_fast The fasta dp_mode using blosum62mt.\r
- ktup Ktup matching (Muscle kind) \r
- aln Read the distances on a precomputed MSA</description>\r
- <optionNames>-distance_matrix_mode</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>very_fast</defaultValue>\r
- <possibleValues>slow</possibleValues>\r
- <possibleValues>fast</possibleValues>\r
- <possibleValues>very_fast</possibleValues>\r
- <possibleValues>ktup</possibleValues>\r
- <possibleValues>aln</possibleValues>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Tree Computation method</name>\r
- <description>\r
- gotoh_pair_wise: implementation of the gotoh algorithm (quadratic in memory and time)\r
- myers_miller_pair_wise: implementation of the Myers and Miller dynamic programming algorithm ( quadratic in time and linear in space). This algorithm is recommended for very long sequences. It is about 2 times slower than gotoh and only accepts tg_mode=1or 2 (i.e. gaps penalized for opening).\r
- fasta_pair_wise: implementation of the fasta algorithm. The sequence is hashed, looking for ktuples words. Dynamic programming is only carried out on the ndiag best scoring diagonals. This is much faster but less accurate than the two previous. This mode is controlled by the parameters -ktuple, -diag_mode and -ndiag\r
- cfasta_pair_wise: c stands for checked. It is the same algorithm. The dynamic programming is made on the ndiag best diagonals, and then on the 2*ndiags, and so on until the scores converge. Complexity will depend on the level of divergence of the sequences, but will usually be L*log(L), with an accuracy comparable to the two first mode ( this was checked on BaliBase). This mode is controlled by the parameters -ktuple, -diag_mode and -ndiag\r
- </description>\r
- <optionNames>-dp_mode</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>cfasta_pair_wise</defaultValue>\r
- <possibleValues>gotoh_pair_wise</possibleValues>\r
- <possibleValues>myers_miller_pair_wise</possibleValues>\r
- <possibleValues>fasta_pair_wise</possibleValues>\r
- <possibleValues>cfasta_pair_wise</possibleValues>\r
- </parameters>\r
-<!-- This should be groupped with -dp_mode -->\r
- <parameters isRequired="false">\r
- <name>Number of diagonals used by the fasta_pair_wise algorithm</name>\r
- <description>\r
- Indicates the number of diagonals used by the fasta_pair_wise algorithm (cf -dp_mode). When -ndiag=0, n_diag=Log (length of the smallest sequence)+1. \r
- When -ndiag and -diag_threshold are set, diagonals are selected if and only if they fulfill both conditions.\r
- </description>\r
- <optionNames>-ndiag</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>0</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>0</min>\r
- <max>1000</max>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Number of diagonals used by the fasta_pair_wise algorithm</name>\r
- <description>\r
- Indicates the manner in which diagonals are scored during the fasta hashing. \r
-0: indicates that the score of a diagonal is equal to the sum of the scores of the exact matches it contains. \r
-1 indicates that this score is set equal to the score of the best uninterrupted segment (useful when dealing with fragments of sequences).\r
- </description>\r
- <optionNames>-diag_mode</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>0</defaultValue>\r
- <possibleValues>0</possibleValues>\r
- <possibleValues>1</possibleValues>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Diagonal threshold</name>\r
- <description>\r
- Sets the value of the threshold when selecting diagonals. \r
- 0: indicates that -ndiag should be used to select the diagonals (cf -ndiag section).\r
- </description>\r
- <optionNames>-diag_threshold</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>0</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>0</min>\r
- <max>1000</max>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Alphabet degeneration method</name>\r
- <description>\r
- Indicates the manner in which the amino acid alphabet is degenerated when hashing in the \r
- fasta_pairwise dynamic programming. Standard ClustalW matrices are all valid. \r
- They are used to define groups of amino acids having positive substitution values. \r
- In T-Coffee, the default is a 13 letter grouping named Vasiliky, with residues grouped as follows:\r
- rk, de, qh, vilm, fy (other residues kept alone).\r
- This alphabet is set with the flag -sim_matrix=vasiliky. \r
- In order to keep the alphabet non degenerated, -sim_matrix=idmat can be used to retain \r
- the standard alphabet.\r
- </description>\r
- <optionNames>-sim_matrix</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>vasiliky</defaultValue>\r
- <possibleValues>vasiliky</possibleValues>\r
- <possibleValues>idmat</possibleValues>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Substitution Matrix</name>\r
- <description>\r
-This flag sets the matrix that will be used by alignment methods within t_coffee (slow_pair, lalign_id_pair). It does not affect external methods (like clustal_pair, clustal_aln). \r
-Users can also provide their own matrices, using the matrix format described in the appendix.\r
- </description>\r
- <optionNames>-matrix</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <possibleValues>blosum62mt</possibleValues>\r
- <!-- This option causes tcoffee to fail \r
- <parameters isRequired="false">\r
- <name>Matrix</name>\r
- <description>Substitution Matrix to use</description>\r
- <optionNames>-matrix</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>BLOSUM62</defaultValue>\r
- <possibleValues>BLOSUM100</possibleValues>\r
- <possibleValues>BLOSUM30</possibleValues>\r
- <possibleValues>BLOSUM35</possibleValues>\r
- <possibleValues>BLOSUM40</possibleValues>\r
- <possibleValues>BLOSUM45</possibleValues>\r
- <possibleValues>BLOSUM50</possibleValues>\r
- <possibleValues>BLOSUM55</possibleValues>\r
- <possibleValues>BLOSUM60</possibleValues>\r
- <possibleValues>BLOSUM62</possibleValues>\r
- <possibleValues>BLOSUM65</possibleValues>\r
- <possibleValues>BLOSUM70</possibleValues>\r
- <possibleValues>BLOSUM75</possibleValues>\r
- <possibleValues>BLOSUM80</possibleValues>\r
- <possibleValues>BLOSUM85</possibleValues>\r
- <possibleValues>BLOSUM90</possibleValues>\r
- <possibleValues>BLOSUMN</possibleValues>\r
- <possibleValues>DAYHOFF</possibleValues>\r
- <possibleValues>GONNET</possibleValues>\r
- <possibleValues>IDENTITY</possibleValues>\r
- <possibleValues>MATCH</possibleValues>\r
- <possibleValues>NUC.4.2</possibleValues>\r
- <possibleValues>NUC.4.4</possibleValues>\r
- <possibleValues>PAM10</possibleValues>\r
- <possibleValues>PAM100</possibleValues>\r
- <possibleValues>PAM110</possibleValues>\r
- <possibleValues>PAM120</possibleValues>\r
- <possibleValues>PAM130</possibleValues>\r
- <possibleValues>PAM140</possibleValues>\r
- <possibleValues>PAM150</possibleValues>\r
- <possibleValues>PAM160</possibleValues>\r
- <possibleValues>PAM170</possibleValues>\r
- <possibleValues>PAM180</possibleValues>\r
- <possibleValues>PAM190</possibleValues>\r
- <possibleValues>PAM20</possibleValues>\r
- <possibleValues>PAM200</possibleValues>\r
- <possibleValues>PAM210</possibleValues>\r
- <possibleValues>PAM220</possibleValues>\r
- <possibleValues>PAM230</possibleValues>\r
- <possibleValues>PAM240</possibleValues>\r
- <possibleValues>PAM250</possibleValues>\r
- <possibleValues>PAM260</possibleValues>\r
- <possibleValues>PAM270</possibleValues>\r
- <possibleValues>PAM280</possibleValues>\r
- <possibleValues>PAM290</possibleValues>\r
- <possibleValues>PAM30</possibleValues>\r
- <possibleValues>PAM300</possibleValues>\r
- <possibleValues>PAM310</possibleValues>\r
- <possibleValues>PAM320</possibleValues>\r
- <possibleValues>PAM330</possibleValues>\r
- <possibleValues>PAM340</possibleValues>\r
- <possibleValues>PAM350</possibleValues>\r
- <possibleValues>PAM360</possibleValues>\r
- <possibleValues>PAM370</possibleValues>\r
- <possibleValues>PAM380</possibleValues>\r
- <possibleValues>PAM390</possibleValues>\r
- <possibleValues>PAM40</possibleValues>\r
- <possibleValues>PAM400</possibleValues>\r
- <possibleValues>PAM410</possibleValues>\r
- <possibleValues>PAM420</possibleValues>\r
- <possibleValues>PAM430</possibleValues>\r
- <possibleValues>PAM440</possibleValues>\r
- <possibleValues>PAM450</possibleValues>\r
- <possibleValues>PAM460</possibleValues>\r
- <possibleValues>PAM470</possibleValues>\r
- <possibleValues>PAM480</possibleValues>\r
- <possibleValues>PAM490</possibleValues>\r
- <possibleValues>PAM50</possibleValues>\r
- <possibleValues>PAM500</possibleValues>\r
- <possibleValues>PAM60</possibleValues>\r
- <possibleValues>PAM70</possibleValues>\r
- <possibleValues>PAM80</possibleValues>\r
- <possibleValues>PAM90</possibleValues>\r
- </parameters>\r
- -->\r
- \r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Match penalty</name>\r
- <description>\r
- Indicates the penalty to associate with a match. When using a library, \r
- all matches are positive or equal to 0. Matches equal to 0 are unsupported by the \r
- library but non-penalized. Setting nomatch to a non-negative value makes it possible \r
- to penalize these null matches and prevent unrelated sequences from being aligned \r
- (this can be useful when the alignments are meant to be used for structural modeling)</description>\r
- <optionNames>-nomatch</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>0</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>0</min>\r
- <max>1000</max>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Gap opening penalty</name>\r
- <description>\r
- Indicates the penalty applied for opening a gap. The penalty must be negative. \r
- If no value is provided when using a substitution matrix, a value will be automatically computed.\r
- Here are some guidelines regarding the tuning of gapopen and gapext. \r
- In T-Coffee matches get a score between 0 (match) and 1000 (match perfectly consistent with the library).\r
- The default cosmetic penalty is set to -50 (5% of a perfect match). \r
- If you want to tune -gapoen and see a strong effect, you should therefore consider values between 0 \r
- and -1000. \r
- </description>\r
- <optionNames>-gapopen</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>0</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>-1000</min>\r
- <max>0</max>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Gap extension penalty</name>\r
- <description>\r
- Indicates the penalty applied for extending a gap. The penalty must be negative. \r
- </description>\r
- <optionNames>-gapext</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>0</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>-1000</min>\r
- <max>0</max>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Cosmetic penalty</name>\r
- <description>\r
- Indicates the penalty applied for opening a gap. The penalty must be negative and is set to a very low value by default.\r
- It will only have an influence on the portions of the alignment that are unalignable. \r
- It will not make them more correct, but only more pleasing to the eye ( i.e. Avoid stretches \r
- of lonely residues). The cosmetic penalty is automatically turned off if a substitution matrix is \r
- used rather than a library.\r
- </description>\r
- <optionNames>-cosmetic_penalty</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>-50</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>-1000</min>\r
- <max>0</max>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Terminal gaps penalty</name>\r
- <description>\r
- 0: terminal gaps penalized with -gapopen + -gapext*len\r
- 1: terminal gaps penalized with a -gapext*len\r
- 2: terminal gaps unpenalized.\r
- </description>\r
- <optionNames>-tg_mode</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>1</defaultValue>\r
- <possibleValues>0</possibleValues>\r
- <possibleValues>1</possibleValues>\r
- <possibleValues>2</possibleValues>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Number of iterations</name>\r
- <description>\r
- Sequences are extracted in turn and realigned to the MSA. \r
- If iterate is set to -1, each sequence is realigned, otherwise the number of iterations is \r
- set by -iterate.\r
- </description>\r
- <optionNames>-iterate</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>0</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>-1</min>\r
- <max>100</max>\r
- </validValue>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Output order</name>\r
- <description>\r
- Sets the order of the sequences in the output alignment: -outorder=input means the sequences \r
- are kept in the original order. -outorder=aligned means the sequences come in the order \r
- indicated by the tree. This order can be seen as a one-dimensional projection of the tree distances. \r
- </description>\r
- <optionNames>-outorder</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>input</defaultValue>\r
- <possibleValues>input</possibleValues>\r
- <possibleValues>aligned</possibleValues>\r
- </parameters>\r
- <parameters isRequired="false">\r
- <name>Input order</name>\r
- <description>\r
- Multiple alignments based on dynamic programming depend slightly on the order in which \r
- the incoming sequences are provided. To prevent this effect sequences are arbitrarily \r
- sorted at the beginning of the program (-inorder=aligned). \r
- However, this affects the sequence order within the library. \r
- You can switch this off by setting -inorder=input\r
- </description>\r
- <optionNames>-inorder</optionNames>\r
- <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
- <defaultValue>aligned</defaultValue>\r
- <possibleValues>input</possibleValues>\r
- <possibleValues>aligned</possibleValues>\r
- </parameters>\r
-</runnerConfig>\r
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
-<presets>\r
- <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
- <preset>\r
- <name>Quick align. Very fast approximate (Speed-oriented)</name>\r
- <description>quickaln: Very fast, sequence type - all, accuracy - medium low</description>\r
- <optlist>\r
- <option>-mode quickaln</option>\r
- </optlist>\r
- </preset>\r
- <!-- does not work\r
- <preset>\r
- <name>Dali (Speed-oriented)</name>\r
- <description>dali: a mode used to combine dali pairwise alignments</description>\r
- <optlist>\r
- <option>-mode dali</option>\r
- </optlist>\r
- </preset>\r
- -->\r
- <!-- This requires Blast to operate, however i do not know how to plug it to t-coffee. \r
- The build in one does not work. \r
- <preset>\r
- <name>3dcoffee (Accuracy-oriented)</name>\r
- <description>3dcoffee: runs t_coffee with the 3dcoffee parameterization</description>\r
- <optlist>\r
- <option>-mode 3dcoffee</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>Accurate (Accuracy-oriented)</name>\r
- <description>accurate: slow, sequence type - protein, accuracy - high</description>\r
- <optlist>\r
- <option>-mode accurate</option>\r
- </optlist>\r
- </preset>\r
- could not find templates(?)\r
- <preset>\r
- <name>Rcoffee for RNA only (accuracy-oriented)</name>\r
- <description> rcoffee: slow, sequence type - RNA, accuracy - high</description>\r
- <optlist>\r
- <option>-mode rcoffee</option>\r
- </optlist>\r
- </preset>\r
- -->\r
- <!-- This needs blast\r
- <preset>\r
- <name>Expresso (accuracy-oriented)</name>\r
- <description> expresso: slow, sequence type - all, accuracy - high</description>\r
- <optlist>\r
- <option>-mode expresso</option>\r
- </optlist>\r
- </preset>\r
- --> \r
-</presets>\r
<body>\r
<div id="page">\r
<div id="banner">\r
- <h2>JABAWS for Developers </h2>\r
+<table> \r
+<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img class="logo" src="images/uod_lt.gif" alt="University of Dundee" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><h2>JABAWS For Developers</h2></td>\r
+</tr>\r
+</table>\r
</div><!-- banner end-->\r
+\r
<div id="wrapper">\r
<div id="panel">\r
- <a class="selected" href="develhome.html">Devel Home</a>\r
- <a href="http://www.compbio.dundee.ac.uk/jaba">JABAWS Production</a>\r
+ <a class="selected" href="index.html">Devel Home</a>\r
+ <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS Production</a>\r
<a href="http://www.compbio.dundee.ac.uk/user/www-jws2/wbstat" title="http://www.compbio.dundee.ac.uk/user/www-jws2/wbstat" rel="nofollow">Webalizer Access Stats</a>\r
<a href="http://www.compbio.dundee.ac.uk/user/www-jws2/awstat_index.html" title="http://www.compbio.dundee.ac.uk/user/www-jws2" rel="nofollow">Awstat Access Stats</a></div>\r
<!-- panel end-->\r
<p>A client package contains only classes from data model layer and a simple web services client. Framework package is for anyone who want to use JABAWS framework for controlling native executables in local or cluster environments. Framework exclude the web services layer. Server package contains all the code.</p>\r
\r
<h4>Running tests</h4>\r
-<p>The test results for the JABAWS package offered for download can be found here: <a href="http://www.compbio.dundee.ac.uk/jaba/tests/index.html">Test Results</a><br/>\r
+<p>The test results for the JABAWS package offered for download can be found here: <a href="http://www.compbio.dundee.ac.uk/user/www-jws2/tests/index.html">Test Results</a><br/>\r
JABAWS uses <a href="http://testng.org/doc/index.html">TestNG</a> for testing. There is a TestNG plugin available for Eclipse which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied with JABAWS together with an ant tasks to run the test cases. </p>\r
<p>The best way to ensure that JABAWS framework is completely functional on your system is to run all test cases. \r
Test cases tests all aspects of JABAWS functionality. Consequently, one need to have non windows operation system and support of the cluster to be able to run all tests. If your system does not support cluster, then you could run all test excluding those that depends on the cluster.\r
<p>JABAWS are the standard JAX-WS web services, which are WS-I basic profile compatible. </p>\r
</div>\r
<!-- content end--> \r
-<div id="copyright">Last update: 7 July 2010<br/>Peter Troshin, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 19 August 2010<br/>Peter Troshin, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
</div> <!-- page end-->\r
-\r
+<!-- Google analitics -->\r
+<script type="text/javascript">\r
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"\r
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
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-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />\r
-<title>Java Bioinformatics Analysis Web Services (JABAWS) download page</title>\r
+<meta name="generator" content="HTML Tidy, see www.w3.org" />\r
+<meta http-equiv="Content-Type" content=\r
+"text/html; charset=iso-8859-1" />\r
+<title>Java Bioinformatics Analysis Web Services (JABAWS) download\r
+page</title>\r
<link href="ws.css" rel="stylesheet" type="text/css" />\r
-<script type="text/javascript" src="prototype-1.6.0.3.js"></script>\r
-\r
+<script type="text/javascript" src="prototype-1.6.0.3.js">\r
+ \r
+</script>\r
</head>\r
<body>\r
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<div id="banner">\r
-<h2><span class="headeru">JA</span>va <span class="headeru">B</span>ioinformatics <span class="headeru">A</span>nalyses <span class="headeru">W</span>eb <span class="headeru">S</span>ervices<h2>\r
-</div><!-- banner end-->\r
+<table> \r
+<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img class="logo" src="images/uod_lt.gif" alt="University of Dundee" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><h2><span class="headeru">JA</span>va <span class=\r
+"headeru">B</span>ioinformatics <span class="headeru">A</span>nalysis <span class="headeru">W</span>eb <span\r
+class="headeru">S</span>ervices</h2></td>\r
+</tr>\r
+</table></div>\r
+\r
+<!-- banner end-->\r
<div id="wrapper">\r
-<div id="panel">\r
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- <a href="manual.html">Manual</a>\r
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- <a class="selected" href="download.html">Download</a>\r
- <a href="http://www.jalview.org">Jalview</a>\r
+<div id="panel"><a href="index.html">Home</a> <a href=\r
+"manual.html">Manual</a> <a href="howto.html">How To</a> <a class=\r
+"selected" href="download.html">Download</a> <a href=\r
+"http://www.jalview.org">Jalview</a>\r
+<a href="http://www.compbio.dundee.ac.uk">Barton Group</a> \r
</div>\r
+\r
<!-- panel end-->\r
<div id="content">\r
-\r
<h4><a name="minclient" id="minclient"></a>JABAWS Client</h4>\r
-<p>\r
-For anyone who would like to program against JABA Web Services or use a command line client.\r
-<a href="http://www.compbio.dundee.ac.uk/jaba/archive/min-jaba-client.jar">Download</a> (64k)</p>\r
+\r
+<p>The client is an executable java archive which provides a\r
+command line client, and can be used by anyone who would like to\r
+program against the JABA Web Services in Java.</p>\r
+\r
+<ul>\r
+<li>JABAWS java client: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client.jar">download</a>\r
+(64k)</li>\r
+</ul>\r
\r
<h4>JABAWS Server</h4>\r
-<p>\r
-Download this if you intend to run JABAWS for your lab/university locally. \r
+\r
+<p>The server is provided as a self-contained web application\r
+archive containing all necessary binaries, ready to install in any\r
+'modern' Java based web application server\r
+<!-- Note - mention servlet 2.4 compliance here? -->. Download this\r
+if you intend to run JABAWS services locally.</p>\r
+\r
<ul>\r
-<li>A Complete Server for all platforms: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba.war">download</a> (45M)</li>\r
-<li>A Complete Server for windows: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-windows.war">download</a> (16M)</li>\r
+<li>A Complete Server for all platforms: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">download</a>\r
+(45M)</li>\r
+\r
+<li>A Complete Server for windows: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-windows.war">download</a>\r
+(16M)</li>\r
</ul>\r
-</p>\r
+\r
\r
<div class="source">\r
-<div class="header collapsed" onclick="$(this).toggleClassName('collapsed'); $(this).next('.body').toggleClassName('collapsed');" title="Click to open/close">Packages for experts</div> <div class="body collapsed">\r
- <h4>JABAWS server without alignment programs</h4>\r
- <p>If you have all the programs or wish to download them separately this package is for you</p>\r
- <p>Complete Server without native executables: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-binaries.war">download</a> (14M) </p>\r
- <h4>JABAWS server without JAX-WS</h4>\r
- <p>\r
- Download this if you intend to run JABAWS for your lab/institute locally. \r
- This package does not contain <a href="https://jax-ws.dev.java.net/">JAX-WS</a> libraries required to run JABAWS. This package is intended for anyone who have JAX-WS libraries already installed on their web application servers. In this case JABAWS will be using the libraries supplied by your web application server. This way you can avoid any version conflicts. </p>\r
- <ul>\r
- <li>Server for all platforms: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-jaxws.war">download</a> (31M)</li>\r
- <li>Server for windows: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-jaxws-windows.war">download</a> (2M)</li>\r
- <li>Server without binaries: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-jaxws-no-binaries.war">download</a> (<1M) </li>\r
- </ul>\r
-\r
-\r
-<h4>JABAWS framework </h4>\r
-<p>\r
-This package is for developers who would like to use JABAWS code to control native executables in local or cluster environments. It is a JABA code without web services part. \r
+<div class="header" onclick=\r
+"$(this).toggleClassName('collapsed'); $(this).next('.body').toggleClassName('collapsed');"\r
+ title="Click to open/close">Packages for experts</div>\r
+\r
+<div class="body">\r
+<h4>JABAWS server without alignment programs</h4>\r
+\r
+<p>If you have all the programs or wish to download them\r
+separately, then this package is for you.</p>\r
+<ul>\r
+ <li>Complete Server without native executables: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-no-binaries.war">\r
+download</a> (14M)</li></ul>\r
+\r
+<h4>JABAWS server without JAX-WS</h4>\r
+\r
+<p>Download this if you intend to run JABAWS for your lab/institute\r
+locally, and have a java web application server which already has\r
+the JAX-WS libraries installed. This package does not contain <a\r
+href="https://jax-ws.dev.java.net/">JAX-WS</a> libraries, so its\r
+installation will not cause any version conflicts.<br />\r
+<em>Note: If you find the server does not work, then we suggest you\r
+try installing the full JABAWS server package.</em></p>\r
+\r
<ul>\r
- <li>A framework package: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/full-jaba-client-pack.zip">download</a>(31M)</li>\r
+<li>Server (without JAX-WS) for all platforms: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-no-jaxws.war">download</a>\r
+(31M)</li>\r
+\r
+<li>Server (without JAX-WS) for windows: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-no-jaxws-windows.war">\r
+download</a> (2M)</li>\r
+\r
+<li>Server (without JAX-WS) without binaries: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-no-jaxws-no-binaries.war">\r
+download</a> (<1M)</li>\r
</ul>\r
-</p>\r
\r
-<h4>A complete source code</h4>\r
-<p>We offer the code under <a href="http://www.apache.org/licenses/LICENSE-2.0.txt">Apache version 2 licence</a> please feel free to download and use our product as well as the source code.\r
-Code comes in the form of an <a href="http://www.eclipse.org">Eclipse</a> project. However, Eclipse is not necessary to run it. Look into build.xml Ant task to find a variety of useful tasks among them are the tasks to run test cases.\r
+<h4>JABAWS execution framework</h4>\r
+\r
+<p>This package is for developers who would like to use JABAWS's\r
+execution system in their own Java programs to control native\r
+executables in local or cluster environments. It is the JABAWS code\r
+without the server components.</p>\r
+\r
<ul>\r
- <li>\r
-A complete eclipse project package: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-project.zip">download</a> (82M)</li>\r
- <li>Source only package: <a href="archive/jaba-source.jar">download</a> (25K) </li>\r
+<li>The framework package: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/full-jaba-client-pack.zip">\r
+download</a>(31M)</li>\r
+</ul> \r
+\r
+<h4>The complete source code</h4>\r
+\r
+<p>We offer the code under <a href=\r
+"http://www.apache.org/licenses/LICENSE-2.0.txt">Apache version 2\r
+licence</a> please feel free to download and use our product as\r
+well as the source code. The code comes in the form of an <a href=\r
+"http://www.eclipse.org">Eclipse</a> project, but Eclipse is not\r
+necessary to run it. Please examine the Ant build file (build.xml)\r
+to find out how to build JABAWS from source, and execute a variety\r
+of useful tasks, including a task for runing the JABAWS test\r
+cases.</p>\r
+\r
+<ul>\r
+<li>A complete eclipse project package: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-project.zip">download</a>\r
+(82M)</li>\r
+\r
+<li>Source only package: <a href=\r
+"archive/jaba-source.jar">download</a> (25K)</li>\r
</ul>\r
-</p>\r
-</div><!--body end -->\r
-</div> <!--source end -->\r
+\r
+<br />\r
+<br />\r
+</div>\r
+\r
+<!--body end -->\r
+</div>\r
+\r
+<!--source end -->\r
+</div>\r
+\r
+<!-- content end-->\r
+<div id="copyright">Last update: 19 August 2010<br />\r
+ Peter Troshin and Geoff Barton, The Barton Group, University of\r
+Dundee, UK</div>\r
</div>\r
-<!-- content end--> \r
-<div id="copyright">Last update: 7 July 2010<br/>\r
-Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
-</div><!-- wrapper end-->\r
-</div> <!-- page end-->\r
+\r
+<!-- wrapper end-->\r
+</div><!-- page end-->\r
+<!-- Google analitics -->\r
+<script type="text/javascript">\r
+var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");\r
+document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));\r
+</script>\r
+<script type="text/javascript">\r
+try{\r
+var pageTracker = _gat._getTracker("UA-5356328-1");\r
+pageTracker._trackPageview();\r
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+</script>\r
\r
</body>\r
</html>\r
</head>\r
<body>\r
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-<div id="banner">\r
-<h2><span class="headeru">JA</span>va <span class="headeru">B</span>ioinformatics <span class="headeru">A</span>nalyses <span class="headeru">W</span>eb <span class="headeru">S</span>ervices</h2>\r
+<div id="banner"><table> \r
+<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img class="logo" src="images/uod_lt.gif" alt="University of Dundee" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><h2><span class="headeru">JA</span>va <span class=\r
+"headeru">B</span>ioinformatics <span class="headeru">A</span>nalysis <span class="headeru">W</span>eb <span\r
+class="headeru">S</span>ervices</h2></td>\r
+</tr>\r
+</table>\r
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<a href="download.html">Download</a>\r
<a href="http://www.jalview.org">Jalview</a>\r
+ <a href="http://www.compbio.dundee.ac.uk">Barton Group</a> \r
</div>\r
<!-- panel end-->\r
<div id="content">\r
<li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a></li>\r
<li><a href="http://www.drive5.com/muscle/download3.6.html">Muscle</a></li>\r
<li><a href="http://www.tcoffee.org/Packages/Binaries/">Tcoffee</a></li>\r
-<li>Probcons (Linux <a href="http://www.compbio.dundee.ac.uk/jaba/archive/binaries/linuxI386/probcons/">I386</a> | <a href="http://www.compbio.dundee.ac.uk/jaba/archive/binaries/linuxAMD64/probcons/">AMD64</a>)</li>\r
+<li>Probcons (Linux <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/binaries/linuxI386/probcons/">I386</a> | <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/binaries/linuxAMD64/probcons/">AMD64</a>)</li>\r
</ul>\r
<p>We would however recommend to compile the binaries for your system whenever possible. This is likely to give you a significant performance gain.</p>\r
<h4><a name="diffbin" id="diffbin"></a>Can I use a different version of the alignment program with JABAWS?</h4>\r
In particular compbio.ws.client.Jws2Client - a command line client <br />\r
compbio.ws.client.WSTester - JABAWS tester. JABAWS source is available from the download page. Please note that for now all the examples are in Java other languages will follow given a sufficient demand. </p>\r
<p>Download jaba <a href="download.html">client library</a>. Add client library to the class path. The following code excerpt will connect your program to Clustal web service deployed in the University of Dundee. </p>\r
-<p class="code"> 1) URL url = new URL("http://www.compbio.dundee.ac.uk/jaba/ClustalWS?wsdl");<br />\r
+<p class="code"> 1) URL url = new URL("http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl");<br />\r
2) QName qname = new QName("http://msa.data.compbio/01/01/2010/", "ClustalWS");<br />\r
3) Service serv = Service.create(url, qname);<br />\r
4) MsaWS<T> msaws = serv.getPort(new QName("http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),\r
<p class="code">((Closeable) msaws).close(); </p>\r
<h4><a name="buildart" id="buildart"></a>Building web services artifacts</h4>\r
<p>JABAWS are the standard JAX-WS SOAP web services, which are WS-I basic profile compatible. This means that you could use whatever tool your language has to work with web services. Below is how you can generate portable artifacts to work with JABAWS from java. Alternatively, from java, you could <a href="#connectto">use the client library</a>. </p>\r
-<p class="code">wsimport -keep http://www.compbio.dundee.ac.uk/jaba/ClustalWS?wsdl</p>\r
+<p class="code">wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl</p>\r
<p>Valid service names are </p>\r
<ul>\r
<li>ClustalWS</li>\r
<p>This should be sufficient to prevent tomcat from removing your JABAWS deployment folder. For more information about tomcat deployer <a href="http://tomcat.apache.org/tomcat-6.0-doc/deployer-howto.html">read this documentation on the tomcat web site</a>.</p>\r
</div>\r
<!-- content end--> \r
-<div id="copyright">Last update: 7 July 2010<br/>\r
+<div id="copyright">Last update: 19 August 2010<br/>\r
Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
</div> <!-- page end-->\r
-\r
+<!-- Google analitics -->\r
+<!-- Google analitics -->\r
+<script type="text/javascript">\r
+var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");\r
+document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));\r
+</script>\r
+<script type="text/javascript">\r
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+pageTracker._trackPageview();\r
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"\r
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
<head>\r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />\r
-<title>Java Bioinformatics Analyses Web Services (JABAWS) main page</title>\r
-<link href="ws.css" rel="stylesheet" type="text/css" media="screen, projection, handheld, tv" />\r
-<link rel="stylesheet" type="text/css" media="print" href="print.css"/>\r
-\r
-<script type="text/javascript" src="prototype-1.6.0.3.js"></script>\r
+<meta name="generator" content="HTML Tidy, see www.w3.org" />\r
+<meta http-equiv="Content-Type" content=\r
+"text/html; charset=iso-8859-1" />\r
+<title>Java Bioinformatics Analyses Web Services (JABAWS) main\r
+page</title>\r
+<link href="ws.css" rel="stylesheet" type="text/css" media=\r
+"screen, projection, handheld, tv" />\r
+<link rel="stylesheet" type="text/css" media="print" href=\r
+"print.css" />\r
+<script type="text/javascript" src="prototype-1.6.0.3.js">\r
+ \r
+</script>\r
</head>\r
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<div id="page">\r
<div id="banner">\r
- <h2><span class="headeru">JA</span>va <span class="headeru">B</span>ioinformatics <span class="headeru">A</span>nalyses <span class="headeru">W</span>eb <span class="headeru">S</span>ervices</h2>\r
-</div><!-- banner end-->\r
+<table> \r
+<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img class="logo" src="images/uod_lt.gif" alt="University of Dundee" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><h2><span class="headeru">JA</span>va <span class=\r
+"headeru">B</span>ioinformatics <span class="headeru">A</span>nalysis <span class="headeru">W</span>eb <span\r
+class="headeru">S</span>ervices</h2></td>\r
+</tr>\r
+</table>\r
+<!-- \r
+Future use?\r
+<div class="uniicon"><a href="http://www.compbio.dundee.ac.uk"><img src="images/uod.gif" alt="University of Dundee, The Barton Group" title="University of Dundee, The Barton Group" longdesc="http://www.compbio.dundee.ac.uk"/></a></div>\r
+-->\r
+</div>\r
+\r
+<!-- banner end-->\r
<div id="wrapper">\r
-<div id="panel">\r
- <a class="selected" href="index.html">Home</a>\r
- <a href="manual.html">Manual</a>\r
- <a href="howto.html">How To</a>\r
- <a href="download.html">Download</a>\r
- <a href="http://www.jalview.org">Jalview</a>\r
+<div id="panel"><a class="selected" href="index.html">Home</a> <a\r
+href="manual.html">Manual</a> <a href="howto.html">How To</a> <a\r
+href="download.html">Download</a> <a href=\r
+"http://www.jalview.org">Jalview</a>\r
+<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a> \r
</div>\r
+\r
<!-- panel end-->\r
<div id="content">\r
-\r
<h4>What is JABAWS?</h4>\r
-<p><span class="u">JA</span>va <span class="u">B</span>ioinformatics <span class="u">A</span>nalysis <span class="u">W</span>eb <span class="u">S</span>ervices (JABAWS) is a collection of <a href="http://www.w3schools.com/SOAP/soap_intro.asp">SOAP</a> web services for bioinformatics. Web services make it easy to access well-known tools from anywhere anytime. SOAP Web Services are designed for use by other programmes, rather than people. Current version of JABA web services integrates with <a href="http://www.jalview.org">Jalview</a> and provides five web services for multiple sequence alignment. They are: </p>\r
+\r
+<p><span class="u">JA</span>va <span class=\r
+"u">B</span>ioinformatics <span class="u">A</span>nalysis <span\r
+class="u">W</span>eb <span class="u">S</span>ervices (JABAWS) is a\r
+collection of <a href=\r
+"http://www.w3schools.com/SOAP/soap_intro.asp">SOAP</a> web\r
+services for bioinformatics.<br />\r
+ JABAWS is designed to make it easy to access bioinformatics\r
+analysis programs over the web, by providing web services, which\r
+make it easy to access programs and databases from anywhere, at\r
+anytime. The flavour of web services that JABAWS provides are SOAP\r
+web services, which are designed for use by other programs, rather\r
+than people.<br />\r
+ The current version of JABAWS is compatible with version 2.6 of <a\r
+href="http://www.jalview.org">Jalview</a>, and provides five web\r
+services for multiple sequence alignment:</p>\r
+\r
<ul>\r
- <li><a href="http://www.clustal.org/">ClustalW</a></li>\r
- <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a></li>\r
- <li><a href="http://www.drive5.com/muscle">Muscle</a></li>\r
- <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a></li>\r
- <li><a href="http://probcons.stanford.edu/">Probcons</a></li>\r
+<li><a href="http://www.clustal.org/">Clustal W</a></li>\r
+\r
+<li><a href=\r
+"http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a></li>\r
+\r
+<li><a href="http://www.drive5.com/muscle">MUSCLE</a></li>\r
+\r
+<li><a href=\r
+"http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">\r
+TCOFFEE</a></li>\r
+\r
+<li><a href="http://probcons.stanford.edu/">PROBCONS</a></li>\r
</ul>\r
+\r
<h4>Why JABAWS?</h4>\r
-<p> JABA Web Services have a number of distinct features not found elsewhere. \r
-<p>In particular JABAWS\r
+\r
+<p>JABA Web Services has a number of distinct features that are not\r
+found in other bioinformatics web services systems. In particular,\r
+JABAWS:</p>\r
+\r
<ol>\r
- <li>gives uniform remote access for a number of command line tools <span class="box"> This allows you to access a number of programmes anywhere anytime. All multiple sequence alignment services comply with a single interface, simplifying command invocation. Most of the command line programmes' options are supported, so you have the same level of control as with the command line. </span></li>\r
- <li>enables Jalview to perform variety of analysis (more to come in the future) on the alignments <span class="box">It is very easy to connect the different instances of JABAWS. So if one is off line, another one will do the job for you. If you use it in your software it is only the matter of a server name change, no other magic is required. </span> </li>\r
- <li>can be easily deployed on a large variety of platforms and run on a single server or on the cluster. <span class="box"><a href="howto.html#clustsubsys">JABAWS integrates with a large number of cluster job management systems.</a>This eliminates the scalability issues and let you focus on your research, JABAWS will take care of the task management. </span></li>\r
- <li> services are <a href="http://www.ws-i.org/">WS-I basic profile</a> v. 1.1 compatible<span class="box">This means that programmes or other web services written in almost any programming languages should have no difficulties using JABA web services.</span></li>\r
- </ol>\r
-<p>Below are the examples of things that you can do with JABAWS</p>\r
+<li>Provides uniform remote access to a number of command line\r
+tools <span class="box">This allows you to access a number of\r
+programs anywhere, at any time. For instance, all multiple sequence\r
+alignment services can be accessed with a single command line\r
+interface, simplifying their invocation. However, most of the\r
+command line options for each program are supported, so you have\r
+nearly the same level of control as if you were running them on the\r
+command line yourself.</span></li>\r
+\r
+<li>Enables web based or stand-alone applications, like Jalview, to\r
+access a variety of bioinformatics analysis methods <span class=\r
+"box">The java web service client library makes it very easy to\r
+connect to one or more instances of JABAWS, so if one server is off\r
+line, all you need to know is the URL of another server that will\r
+do the job for you.<br />\r
+JABAWS provides <a href="http://www.ws-i.org/">WS-I basic\r
+profile</a> v. 1.1 compatible services, which means that clients\r
+can be created for them in almost any programming\r
+language.</span></li>\r
+\r
+<li>Can be easily deployed as a server on a variety of platforms,\r
+with command line tools run on the same machine or on a\r
+cluster.<span class="box"><a href="howto.html#clustsubsys">JABAWS\r
+integrates with a number of cluster job management systems (e.g.\r
+GridEngine, PBS, LSF, Condor).</a> It also intelligently manages\r
+task scheduling depending on their size, eliminatng the scalability\r
+issues and let you focus on your research.</span></li>\r
+</ol>\r
+\r
+<p>Here are just some of the problems that JABAWS can solve:</p>\r
+\r
<ul>\r
- <li>\r
- <p><strong>Unhappy with the defaults settings? </strong><br /> \r
- Want to use PAM200 substitution matrix, set the number of iterations, or sequence clustering method? No problems, JABAWS can do that. Any additional parameters or combinations of where of can be defined. You are no longer limited to defaults!</p>\r
- </li>\r
- <li>\r
- <p><strong>JABAWS in Dundee is not available? </strong>No problem, choose a different service provider and off you go. We hope that other major service providers like EBI will soon be housing JABAWS. </p>\r
- </li>\r
- <li>\r
- <p><strong>Worried about sending your data to the internet?</strong> Install JABAWS in your lab. Point your Jalview client to the services in your lab, and no data will leave you lab any longer.</p>\r
- </li>\r
- <li>\r
- <p><strong>Want to install JABAWS but are not sure what is required? </strong>JABA Web Services will work happily on a single server as well as on the cluster. For large number of request of cause it is better to use a cluster. Little configuration is involved. </p>\r
- </li>\r
- </ul>\r
-<h3> Public JABAWS Server</a></h3>\r
- <table>\r
- <tbody>\r
- <tr>\r
- <th> Feature </th>\r
- <th> Description </th>\r
- </tr>\r
- <tr>\r
- <td><acronym title="Uniform Resource Locator">URL</acronym> </td>\r
- <td><a href="http://www.compbio.dundee.ac.uk/jaba" title="http://www.compbio.dundee.ac.uk/jaba" rel="nofollow">http://www.compbio.dundee.ac.uk/jaba</a> </td>\r
- </tr>\r
- <tr>\r
- <td> Execution limits </td>\r
- <td> Local execution limit is 40 sequnces with no more than 500 letters average length. Larger tasks are send to the cluster. Tasks exceeding 1000×1000 (sequences per letters) will not be accepted for alignment. If you would like to work with bigger alignments consider installing JABAWS in your lab. </td>\r
- </tr>\r
- <tr>\r
- <td> Web Services Description </td>\r
- <td><a href="http://www.compbio.dundee.ac.uk/jaba/ClustalWS?" title="http://www.compbio.dundee.ac.uk/jaba/ClustalWS?" rel="nofollow">WSDL List</a> </td>\r
- </tr>\r
- </tbody>\r
- </table>\r
+<li>\r
+<p><strong>The default settings for a program don't work for my\r
+data!</strong><br />\r
+ JABAWS includes a comprehensive parameter model and validation\r
+mechanism, allowing you to specify additional options and\r
+arguments. Want to use PAM200 substitution matrix, set the number\r
+of iterations, or sequence clustering method? No problem - JABAWS\r
+lets you do that. You are no longer limited to defaults!</p>\r
+</li>\r
+\r
+<!--<li>\r
+ <p><strong>JABAWS in Dundee is not available?</strong> No problem,\r
+ choose a different service provider and off you go. We hope that\r
+ other major service providers like EBI will soon be housing\r
+ JABAWS.</p>\r
+ </li> -->\r
+<li>\r
+<p><strong>I don't want to send my data to the\r
+internet!</strong><br />\r
+ Simply <a href="download.html">download</a> and <a href=\r
+"howto.html#hdjaba">install</a> JABAWS on a trusted machine in your\r
+lab or institute, and use its web address instead of the public\r
+JABAWS services. No data will leave your lab any longer.</p>\r
+</li>\r
+\r
+<li>\r
+<p><strong>Running programs using the public services is slower\r
+than using my own computer!</strong><br />\r
+ The JABAWS server can run programs on a single machine or on a\r
+cluster, and are <a href="howto.html#hdjaba">easy to install</a>.\r
+If your server is going to be heavily used, then it is better to <a\r
+href="howto.html#clustsubsys">configure JABAWS to access your\r
+cluster</a>, which is straightforward.</p>\r
+</li>\r
+</ul>\r
+\r
+<h3>Public JABAWS Server</h3>\r
+\r
+<table>\r
+<tbody>\r
+<tr>\r
+<th>Feature</th>\r
+<th>Description</th>\r
+</tr>\r
+\r
+<tr>\r
+<td><acronym title="Uniform Resource Locator">URL</acronym> </td>\r
+<td><a href="http://www.compbio.dundee.ac.uk/jabaws" title=\r
+"http://www.compbio.dundee.ac.uk/jabaws" rel=\r
+"nofollow">http://www.compbio.dundee.ac.uk/jabaws</a> </td>\r
+</tr>\r
+\r
+<tr>\r
+<td>Execution limits</td>\r
+<td>Local execution limit is 40 sequnces with no more than 500\r
+letters average length. Larger tasks are send to the College of\r
+Life Sciences HPC cluster. Tasks exceeding 1000×1000\r
+(sequences per letters) will not be accepted for alignment. If you\r
+would like to work with bigger alignments consider installing\r
+JABAWS in your lab.</td>\r
+</tr>\r
+\r
+<tr>\r
+<td>Web Services Description</td>\r
+<td><a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?"\r
+title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=\r
+"nofollow">WSDL List</a> </td>\r
+</tr>\r
+</tbody>\r
+</table>\r
\r
<h4>Authors</h4>\r
-<p>Conceptually, Java Bioinformatics Analysis Web Services are the successor of the Jalview Web Services. At the code level, however, JABA Web Services do not contain any code from Jalview Web Services because of the complete change of technologies in time of coding. Jim Procter and Geoff Barton are the authors of Jalview Web Services. Peter Troshin and Geoff Barton are the authors of the JABA Web Services. Jim Procter has contributed to JABAWS development by making useful suggestions, integrating JABAWS with Jalview, and correcting some of its configuration files.</p>\r
-</div><!-- content end--> \r
-<div id="copyright">Last update: 9 July 2010<br/>\r
-Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
-</div><!-- wrapper end-->\r
-</div> <!-- page end-->\r
\r
+<p>Peter Troshin and Geoff Barton are the authors of the JABA Web\r
+Services. Jim Procter helped with the JABAWS design process and web\r
+pages, and developed the interface and management components in\r
+Jalview to access JABAWS servers.</p>\r
+</div>\r
+\r
+<!-- content end-->\r
+<div id="copyright">Last update: 19 August 2010<br />\r
+ Peter Troshin and Geoff Barton, The Barton Group, University of\r
+Dundee, UK</div>\r
+</div>\r
+\r
+<!-- wrapper end-->\r
+</div>\r
+<!-- Google analitics -->\r
+<script type="text/javascript">\r
+var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");\r
+document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));\r
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+<script type="text/javascript">\r
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-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />\r
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-<h2><span class="headeru">JA</span>va <span class="headeru">B</span>ioinformatics <span class="headeru">A</span>nalyses <span class="headeru">W</span>eb <span class="headeru">S</span>ervices</h2>\r
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+<table> \r
+<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img class="logo" src="images/uod_lt.gif" alt="University of Dundee" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><h2><span class="headeru">JA</span>va <span class=\r
+"headeru">B</span>ioinformatics <span class="headeru">A</span>nalysis <span class="headeru">W</span>eb <span\r
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+<div id="panel"><a href="index.html">Home</a> <a class="selected"\r
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+<a href="http://www.compbio.dundee.ac.uk">Barton Group</a> \r
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+\r
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-\r
-\r
<h2>JABAWS Manual</h2>\r
+\r
<h4>JABAWS Installation</h4>\r
-<p>JABA web services require Java 6 to function. We recommend using Sun Java Virtual Machine. JABAWS can be deployed on any Servlet 2.4 compatible web application server. We have tested JABA on the Apache-Tomcat version 6 web application container, however, version 5.5 should do as well. To deploy JABAWS follow your web application server specific deployment procedures. For Apache-Tomcat just drop the war file into webapps directory. Tomcat will do the rest. At this point you should have JABA web services up and running on windows machines. There are more steps to do if you are deploying JABAWS on other operation systems. </p>\r
-<p>JABA web services depend on the alignment programs to do the actual alignment, so it must have an access to the alignment programs which can be executed on your platform. JABAWS is bundled with native windows executables, native Linux i386 executables, and the source code for all alignment programs JABAWS wraps. If you are installing it on Linux should not worry about installing the alignment programmes, the ones that comes with JABAWS should work. For any other operation systems you need to make the alignment programs available to JABAWS. </p>\r
-<p>If you are installing on Linux it may be just a matter of setting executable flag for the binaries bundled with JABAWS. There is a script which would help you with that. To use it cd to <span class="hightlight"><webapplicationpath>/binaries/src</span> and run <span class="hightlight">sh setexecflag.sh</span> script. Restart the Tomcat. That is it JABAWS should work at this point. If not read on... or have a look at <a href="howto.html#usingtomcat">deploying on Tomcat </a>tips. You may want to enable logging, <a href="#logfiles">see below how to do that</a>. </p>\r
-<h4>Making Alignment Programs Available to JABAWS </h4>\r
-<p>There are three possible solutions for this problem</p>\r
-<ul>\r
- <li>Reuse the binaries that are already have in your system</li>\r
- <li> Use bundled with JABAWS alignment programs</li>\r
- <li> Obtain the alignment programs for your OS elsewhere</li>\r
-</ul>\r
-<p>They are described in greater details below </p>\r
-<p><strong><a name="haveexec" id="haveexec"></a>If you would like to use the binaries you already have </strong></p>\r
-<p> Than you just need to let JABAWS know there they are. For this edit <span class="code">conf/Executable.properties </span>file. Please provide an absolute path to each executable in your system. For example default path for clustalw executable is defined as <span class="code">local.clustalw.bin=binaries/src/clustalw/src/clustalw2</span> replace it with absolute path to executable in your system. Instead of changing <span class="hightlight">Executable.properties</span> you could replace executables bundled with JABAWS with the once you have. Then the default configuration will work for you. If you like to find out more about <span class="hightlight">Executable.properties</span> file <a href="#exec">see below</a>. </p>\r
-<p><strong>If you would like to use bundled with JABAWS alignment programs </strong></p>\r
+\r
+<h5>System Requirements</h5>\r
+\r
+<p>JABAWS requires a java web application server compliant with\r
+version 2.4 of the java servlet specification, and a java 6 runtime\r
+environment. We recommend using an official Sun Java 6 runtime\r
+environment, but others may work. We have tested JABAWS with <a\r
+href="http://tomcat.apache.org/download-60.cgi">Apache-Tomcat\r
+version 6</a>, however we expect it will also be compatible with <a\r
+href="http://tomcat.apache.org/download-55.cgi">version\r
+5.5</a>.</p>\r
+\r
+<!-- todo: link to help about obtaining and installing tomcat -->\r
+<h5>Installing the JABAWS WAR file</h5>\r
+\r
+<p>JABAWS is distributed as a web application archive (WAR). To\r
+deploy JABAWS in Apache-Tomcat - simply drop the war file into the\r
+<span class="highlight">webapps</span> directory of a running\r
+Tomcat, and it will do the rest. For any other web application\r
+server, please follow your server's specific deployment procedure\r
+for 'WAR' files. If you are installing on a windows machine, then\r
+at this point your JABAWS installation will already be up and\r
+running, and you can try its services out using the <a href=\r
+"howto.html#usingWsTester">JABAWS test client</a>, but\r
+installations on other operating systems will require a final step\r
+to ensure JABAWS can locate and execute the binary programs it\r
+needs.</p>\r
+\r
+<h4>Preparing executables for use with JABAWS</h4>\r
+\r
+<p>JABAWS's web services use command line programs to do\r
+the actual analysis, so it must have access to programs\r
+which can be executed on your platform. The native executables\r
+bundled with JABAWS for Windows (32-bit) and Linux (i386) should be\r
+OK for those systems. However, the source code for these \r
+programs is also provided so you can recompile for your own\r
+architecture and exploit any optimisations that your system can\r
+provide. Alternately, if you have already got binaries on your\r
+system, then you can simply change the paths in JABAWS's\r
+configuration files so these are used instead.</p>\r
+\r
+<h5>Using the pre-compiled i386 binaries on Linux</h5>\r
+\r
+<p>Before the binaries that are bundled with JABAWS can be used,\r
+they must first be made executable using the provided <a name=\r
+"setexecflag" id="setexecflag">'setexecflag.sh'</a> script:</p>\r
+\r
<ol>\r
- <li><a name="setexecflag" id="setexecflag"></a> Set executable flag for binaries. For this you could use the script provided. <span class="hightlight">cd</span> to <span class="hightlight">binaries/src</span><br /> \r
- run <span class="hightlight">setexecflag.sh</span> script. </li>\r
- <li>Make sure binaries supplied work under your OS. For this run each binary. You do not need any input or flags. If you see a error message complaining about missing libraries or other problems with an executable itself rather than with an input, you need to (a) recompile the binary.\r
- <ul>\r
- <li> To recompile all the binaries for your system you could use a script supplied with the JABAWS. <br />\r
- For this cd to folder<span class="hightlight"> binaries/src</span> execute script compilebin.sh \r
- (either chmod +x it or sh compilebin.sh)</li>\r
- <li>Makes sure everything compiled and work<br />\r
- correctly performing first part of a step 2 again. </li>\r
- <li>If not everything compiled then, it may be that your system does not have all the tools required for recompilation. At a very least check that you have gcc, g++ and make installed in your system. If not install these packages and repeat step (a). </li>\r
- <li>If compilation fails with unclear reason, try obtaining the <a href="#obtainexec">pre compiled binaries</a> for your OS</li>\r
- </ul>\r
- </li>\r
- <li>Consider recompiling all binaries for your platform, this is likely to give you a performance increase. </li>\r
+<li>cd to <span class=\r
+"hightlight"><webapplicationpath>/binaries/src</span></li>\r
+\r
+<li>run <span class="hightlight">sh setexecflag.sh</span></li>\r
+\r
+<li>Make sure binaries supplied work under your OS.<br />\r
+ For this run each binary, without any command line options or\r
+input files. If you see an error message complaining about missing\r
+libraries or other problems, then you probably need to <a href=\r
+"#recompbinaries">recompile the binaries</a>. with</li>\r
+\r
+<li>Restart the Tomcat.</li>\r
</ol>\r
-<p><strong><a name="obtainexec" id="obtainexec"></a>Obtain alignment program for your operation system elsewhere </strong></p>\r
-<p>You could search for pre-packaged compiled executable in your system package repository or try downloading compiled version from alignment program's home page. Then, executables supplied with the system can be replaced with downloaded or new path to the executable can be defined in <span class="hightlight">executable.properties</span> as described above.</p>\r
-<h4>Default JABA Web Services Configuration</h4>\r
-<p>By default JABAWS configured with local engine enabled and an output directory called "jobsout" within web application itself. This will give you a working copy of JABAWS straight after the deployment. You may be interested to know what is the the <a href="#warfile">war file</a>.</p>\r
-<h4>JABAWS Configuration Details </h4>\r
-There are three part of the system you can configure. The local and cluster engines and individual executables. \r
+\r
+That's it! JABAWS should work at this point. Try it out using the<a\r
+href="howto.html#usingWsTester">JABAWS test client</a>. If not,\r
+read on... or have a look at <a href=\r
+"howto.html#usingtomcat">deploying on Tomcat</a> tips.<br />\r
+ <em>Note: You may want to enable logging, <a href="#logfiles">see\r
+below for instructions on how to do that</a>.</em><br />\r
+ \r
+\r
+<h5><a name="recompbinaries">Recompiling the bundled\r
+programs for your system</a></h5>\r
+\r
+<p>If you have a fully equipped build environment on your\r
+(POSIX-like) system, then you should be able to recompile the\r
+programs from the source distributions which are included\r
+in the JABAWS war file. A script called 'compilebin.sh' is provided\r
+to automate this task.</p>\r
+\r
+<ol>\r
+<li>In a terminal window, change the working directory to <span\r
+class="hightlight">binaries/src</span></li>\r
+\r
+<li>execute the <span class="highlight">compilebin.sh</span>\r
+script,<br />\r
+ either use: <span class="hightlight">chmod +x compilebin.sh;\r
+compilebin.sh > compilebin.out;</span><br />\r
+ or: <span class="hightlight">sh compilebin.sh >\r
+compilebin.out</span></li>\r
+\r
+<li>Now run <span class="hightlight">sh setexecflag.sh</span><br />\r
+ If any of the binaries was not recompiled, then a 'file not found'\r
+error will be raised.</li>\r
+\r
+<li>Finally, restart your tomcat (or servlet container), and use\r
+the <a href="howto.html#usingWsTester">JABAWS test client</a> to\r
+check that JABAWS can use the new binaries.</li>\r
+</ol>\r
+\r
+<p>If you couldn't compile everthing, then it may be that your system does\r
+not have all the tools required for compiling the programs. At the very\r
+least check that you have gcc, g++ and make installed in your\r
+system. If not install these packages and repeat the compilation\r
+steps again. You should also review the compilebin.sh output -\r
+which was redirected to compilebin.out, and any errors output to\r
+the terminal. Finally, try obtaining the <a href="#obtainexec">pre\r
+compiled binaries</a> for your OS.</p>\r
+\r
+<h5><a name="haveexec" id="haveexec">Reuse the binaries that are\r
+already in your system</a></h5>\r
+\r
+<p>If you would like to use the binaries you already have then you\r
+just need to let JABAWS know there they are. To do this, edit:\r
+<span class="code">conf/Executable.properties</span>\r
+<p>When specifying paths to executables that already exist on your system, make sure you provide an absolute path, or one relative to the JABAWS directory inside <span class="highlight">webapps</span>. For example, the default path for clustalw is defined\r
+as<span class=\r
+"code">local.clustalw.bin=binaries/src/clustalw/src/clustalw2</span>\r
+Alternatively, instead of changing <span class=\r
+"hightlight">Executable.properties</span> you could also replace\r
+the executables bundled with JABAWS with the ones that you have, or make symlinks to them.\r
+Then the default configuration will work for you. More information\r
+about <a href="#exec"><span class="hightlight">the\r
+Executable.properties</span> file is given below</a>.</p>\r
+\r
+<h5><a name="obtainexec" id="obtainexec">Obtaining alignment\r
+programs for your operation system from elsewhere</a></h5>\r
+\r
+<p>You could search for pre-packaged compiled executable in your\r
+system package repository or alternately, download pre-compiled\r
+binaries from each alignment program's home page. Then, either\r
+replace the executables supplied with the downloaded ones, or\r
+modify the paths in <span class=\r
+"hightlight">executable.properties</span> as described above.</p>\r
+\r
+<h4>Configuring JABAWS</h4>\r
+\r
+<p>There are three parts of the system you can configure. The local\r
+and cluster engines, and the paths to individual executables for\r
+each engine. These settings are stored in configuration files\r
+within the web application directory (for an overview, then take a\r
+look at the <a href="#warfile">war file content table</a>).</p>\r
+\r
+<h5>Default JABA Web Services Configuration</h5>\r
+\r
+<p>Initially, JABAWS is configured with only the local engine\r
+enabled, with job output written to directory called "jobsout"\r
+within the web application itself. This means that JABAWS will work\r
+out of the box, but may not be suitable for serving a whole lab or\r
+instute.</p>\r
+\r
<h4>Local Engine Configuration</h4>\r
-<p>\r
-Local engine configuration is achieved by changing settings in the properties file conf/Engine.local.properties.\r
-Supported configuration settings are: \r
-<br/>\r
-<span class="hightlight">engine.local.enable=true</span> - # enable or disable local engine, valid values true | false\r
-<br/>\r
-<span class="hightlight">local.tmp.directory=D:\\clusterengine\\testoutput </span>- a directory to use for temporary files storage, optional, defaults to java temporary directory \r
-<br/>\r
-<span class="hightlight">engine.local.thread.number=4</span> - Number of threads for tasks execution (valid values between 1 and 2x cpu. Where x is a number of cores available in the system). Optional defaults to the number of cores for core number <=4 and number of cores-1 for greater core numbers.</p>\r
-<p>If you are planning to use local engine (which you have to if you do not have a cluster) it is a good idea to increase the amount of memory available for the web application server. Apache-Tomcat will be happy to take its memory settings from JAVA_OPTS environmental variable. We would recommend using Sun Java Virtual Machine (JVM) in preference to Open JDK. To specify which JVM to use for Apache-Tomcat just define a JAVA_HOME environmental variable. Below is an example of code which can be added to <span class="hightlight"><tomcat_dir>/bin/setenv.sh</span> script to define which JVM to use and a memory settings for Tomcat server. Tomcat server startup script (<span class="hightlight">catalina.sh</span>) will execute <span class="hightlight">setenv.sh</span> on each server start automatically. <br />\r
- <span class="code">export JAVA_HOME=/homes/ws-dev2/jdk1.6.0_17/<br />\r
- export JAVA_OPTS="-server -Xincgc -Xms512m -Xmx1024m"</span></p>\r
+\r
+<p>The Local execution engine configuration is defined in the\r
+properties file conf/Engine.local.properties. The supported\r
+configuration settings are:<br />\r
+ <span class="hightlight">engine.local.enable=true</span> - #\r
+enable or disable local engine, valid values true | false<br />\r
+ <span class=\r
+"hightlight">local.tmp.directory=D:\\clusterengine\\testoutput</span>\r
+- a directory to use for temporary files storage, optional,\r
+defaults to java temporary directory<br />\r
+ <span class="hightlight">engine.local.thread.number=4</span> -\r
+Number of threads for tasks execution (valid values between 1 and\r
+2x cpu. Where x is a number of cores available in the system).\r
+Optional defaults to the number of cores for core number <=4 and\r
+number of cores-1 for greater core numbers.</p>\r
+\r
+<p>If you are planning to heavily use the local engine (which you\r
+have to if you do not have a cluster) it is a good idea to increase\r
+the amount of memory available for the web application server. If\r
+you are using Apache-Tomcat, then you can define its memory\r
+settings in the JAVA_OPTS environment variable. To specify which\r
+JVM to use for Apache-Tomcat, put the full path to the JRE\r
+installation in the JAVA_HOME environment variable (We would\r
+recommend using Sun Java Virtual Machine (JVM) in preference to\r
+Open JDK). Below is an example of code which can be added to <span\r
+class="hightlight"><tomcat_dir>/bin/setenv.sh</span> script\r
+to define which JVM to use and a memory settings for Tomcat server.\r
+Tomcat server startup script (<span class=\r
+"hightlight">catalina.sh</span>) will execute <span class=\r
+"hightlight">setenv.sh</span> on each server start\r
+automatically.<br />\r
+ <span class="code">export\r
+JAVA_HOME=/homes/ws-dev2/jdk1.6.0_17/<br />\r
+ export JAVA_OPTS="-server -Xincgc -Xms512m -Xmx1024m"</span></p>\r
+\r
<h4>Cluster Engine Configuration</h4>\r
-<p>Supported configuration settings: <br/>\r
-<span class="hightlight">engine.cluster.enable=true</span> - # enable or disable local engine true | false, defaults to false\r
-<br/>\r
-<span class="hightlight">cluster.tmp.directory=/homes/clustengine/testoutput- </span>a directory to use for temporary files storage. The value must be an absolute path to the temporary directory. Required. The value must be different from what is defined for local engine. This directory must be accessible from all cluster nodes. <br />\r
-For the cluster engine to work SGE_ROOT and LD_LIBRARY_PATH environmental variable have to be defined. They tell the cluster engine where to find DRMAA libraries. These environmental variables should be defined on the web application server e.g. </p>\r
+\r
+<p>Supported configuration settings:<br />\r
+ <span class="hightlight">engine.cluster.enable=true</span> - #\r
+enable or disable local engine true | false, defaults to\r
+false<br />\r
+ <span class=\r
+"hightlight">cluster.tmp.directory=/homes/clustengine/testoutput-</span>\r
+a directory to use for temporary files storage. The value must be\r
+an absolute path to the temporary directory. Required. The value\r
+must be different from what is defined for local engine. This\r
+directory must be accessible from all cluster nodes.<br />\r
+ For the cluster engine to work, the SGE_ROOT and LD_LIBRARY_PATH\r
+environment variables have to be defined. They tell the cluster\r
+engine where to find DRMAA libraries. These variables\r
+should be defined when the web application server starts up, e.g.</p>\r
+\r
<p><span class="code">SGE_ROOT=/gridware/sge<br />\r
- LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64</span></p>\r
-<p>Finally, do not forget to configure executables for the cluster execution, they may be the same as for the local execution but may be different. Please refer to the executable configuration section for further details. </p>\r
+ LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64</span></p>\r
+\r
+<p>Finally, do not forget to configure executables for the cluster\r
+execution, they may be the same as for the local execution but may\r
+be different. Please refer to the executable configuration section\r
+for further details.</p>\r
+\r
<h4><a name="exec" id="exec"></a>Executable Configuration</h4>\r
-<p>All executables, the binary multiple sequence alignment programs are configured in conf/Executable.properties file. Each executable configured with a number of options they are: \r
-<span class="code">\r
- local.X.bin.windows=<path to executable under windows system, optional>\r
- <br/>local.X.bin=<path to the executable under non-windows system, optional>\r
- <br/>cluster.X.bin=<path to the executable on the cluster, all cluster nodes must see it, optional>\r
- <br/>X.bin.env=<semicolon separated list of environmental variables for executable, use hash symbol as name value separator, optional>\r
- <br/>X.--aamatrix.path=<path to the directory containing substitution matrices, optional>\r
- <br/>X.presets.file=<path to the preset configuration file, optional >\r
- <br/>X.parameters.file=<path to the parameters configuration file, optional> \r
- <br/>X.limits.file=<path to the limits configuration file, optional>\r
- <br/>X.cluster.settings=<list of the cluster specific options, optional></span></p>\r
-<p>\r
- Where X is a short executable wrapper class name. </p>\r
-<p>Default JABAWS configuration includes path to local executables to be run by the local engine only, all cluster related settings are commened out, but they are there for you as example. Cluster engine is disabled by default. To configure executable for cluster execution uncomment the X.cluster settings and change them appropriately.<br/>\r
- For example a complete Mafft configuration may look like this:<span class="code" > local.mafft.bin.windows=\r
- <br/>\r
- local.mafft.bin=binaries/mafft\r
- <br/>cluster.mafft.bin=/homes/cengine/mafft\r
- <br/>mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;\r
- <br/>mafft.--aamatrix.path=binaries/matrices\r
- <br/>mafft.presets.file=conf/settings/MafftPresets.xml\r
- <br/>mafft.parameters.file=conf/settings/MafftParameters.xml\r
- <br/>mafft.limits.file=conf/settings/MafftLimits.xml\r
- <br/>mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M</span>\r
-<p>Please not that relative paths must only be specified for the files that reside inside web application directory, all other paths must be supplied as absolute! </p>\r
-<p>Unfortunately, it is unsafe to modify environmental variable values, thus you need to specify the absolute path to anything defined as environment variable. </p>\r
-<p>If you are using JABAWS to submit jobs to the cluster (with cluster engine enabled), executables must be available from all cluster nodes the task can be sent to, also paths to the executables on the cluster e.g. <span class="hightlight">cluster.<exec_name>.bin</span> must be absolute. </p>\r
-<p>Executables can be located anywhere in your system, they do not have to reside on the server as long as the web application server can access and execute them. </p>\r
-<p>Cluster settings are treated as a black box, the system will just pass whatever is specified in this line directly to the cluster submission library. This is how DRMAA itself treats this settings. More exactly DRMAA JobTemplate.setNativeSpecification() function will be called. </p>\r
-<h5><a name="setexecenv"/>Defining Environmental Variables for Executable</h5>\r
-<p>Environmental variables can be defined in property <span class="code">x.bin.env</span> Where <span class="hightlight">x</span> is one of five executables supported by JABAWS. Several environmental variables can be specified in the same line. For example. <br />\r
- <span class="code" >mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;</span></p>\r
-<p>The example above define two environmental variables with names MAFFT-BINARIES and FASTA_4_MAFFT and values /homes/cengine/mafft and /bin/fasta34 respectively. Semicolon is used as a separator between different environment variables whereas hash is used as a separator for name and value of the variable. </p>\r
-<h4><a name="mafftconf" id="mafftconf"></a>Configure JABAWS to Work with Mafft </h4>\r
-<p>If you use default configuration you do not need to read any further. The default configuration will work for you without any changes, however, if you want to install Mafft yourself then there is a couple of more steps to do. </p>\r
-<p>Mafft executable needs to know the location of other files supplied with Mafft. In addition some Mafft functions depends on the fasta executable, which is not supplied with Mafft, but is a separate package. Mafft needs to know the location of fasta34 executable. </p>\r
-<p>To let Mafft know where the other files from its package are change the value of MAFFT-BINARIES environmental variable. To let Mafft know where is the fasta34 executable set the value of FASTA_4_MAFFT environment variable to point to a location of fasta34 program. The latter can be added to the PATH variable instead. If you are using executables supplied with JABAWS, the path to Mafft binaries would be like <span class="hightlight"><relative path to web application directory>/binaries/src/mafft/binaries</span> and the path to fasta34 binary would be <span class="hightlight"><relative path to web application directory>/binaries/src/fasta34/fasta34</span>. You can specify the location of Mafft binaries as well as fasta34 program elsewhere by providing an absolute path to them. All these settings are defined in <span class="hightlight">conf/Executable.properties</span> file.</p>\r
+\r
+<p>All the executable programs\r
+are configured in conf/Executable.properties file. Each executable\r
+is configured with a number of options. They are: <span class=\r
+"code">local.X.bin.windows=<path to executable under windows\r
+system, optional><br />\r
+ local.X.bin=<path to the executable under non-windows system,\r
+optional><br />\r
+ cluster.X.bin=<path to the executable on the cluster, all\r
+cluster nodes must see it, optional><br />\r
+ X.bin.env=<semicolon separated list of environment variables\r
+for executable, use hash symbol as name value separator,\r
+optional><br />\r
+ X.--aamatrix.path=<path to the directory containing\r
+substitution matrices, optional><br />\r
+ X.presets.file=<path to the preset configuration file, optional\r
+><br />\r
+ X.parameters.file=<path to the parameters configuration file,\r
+optional><br />\r
+ X.limits.file=<path to the limits configuration file,\r
+optional><br />\r
+ X.cluster.settings=<list of the cluster specific options,\r
+optional></span></p>\r
+\r
+<p>Where X is a short executable wrapper class name.</p>\r
+\r
+<p>Default JABAWS configuration includes path to local executables\r
+to be run by the local engine only, all cluster related settings\r
+are commened out, but they are there for you as example. Cluster\r
+engine is disabled by default. To configure executable for cluster\r
+execution uncomment the X.cluster settings and change them\r
+appropriately.<br />\r
+ For example a complete Mafft configuration may look like\r
+this:<span class="code">local.mafft.bin.windows=<br />\r
+ local.mafft.bin=binaries/mafft<br />\r
+ cluster.mafft.bin=/homes/cengine/mafft<br />\r
+ mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;<br />\r
+ mafft.--aamatrix.path=binaries/matrices<br />\r
+ mafft.presets.file=conf/settings/MafftPresets.xml<br />\r
+ mafft.parameters.file=conf/settings/MafftParameters.xml<br />\r
+ mafft.limits.file=conf/settings/MafftLimits.xml<br />\r
+ mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l\r
+h_vmem=6000M -l ram=6000M</span></p>\r
+\r
+<p>Please not that relative paths must only be specified for the\r
+files that reside inside web application directory, all other paths\r
+must be supplied as absolute!</p>\r
+\r
+<p>Furthermore, you should avoid using environment variables within the paths or options - since these will not be evaluated correctly. Instead, please explicitly\r
+specify the absolute path to anything\r
+normally evaluated from an environment variable at execution time.</p>\r
+\r
+<p>If you are using JABAWS to submit jobs to the cluster (with\r
+cluster engine enabled), executables must be available from all\r
+cluster nodes the task can be sent to, also paths to the\r
+executables on the cluster e.g. <span class=\r
+"hightlight">cluster.<exec_name>.bin</span> must be\r
+absolute.</p>\r
+\r
+<p>Executables can be located anywhere in your system, they do not\r
+have to reside on the server as long as the web application server\r
+can access and execute them.</p>\r
+\r
+<p>Cluster settings are treated as a black box, the system will\r
+just pass whatever is specified in this line directly to the\r
+cluster submission library. This is how DRMAA itself treats this\r
+settings. More exactly DRMAA JobTemplate.setNativeSpecification()\r
+function will be called.</p>\r
+\r
+<h5><a name="setexecenv" />Defining Environment Variables for\r
+Executables</h5>\r
+\r
+<p>Environment variables can be defined in property <span class=\r
+"code">x.bin.env</span> Where <span class="hightlight">x</span> is\r
+one of five executables supported by JABAWS. Several environment\r
+variables can be specified in the same line. For example.<br />\r
+ <span class=\r
+"code">mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;</span></p>\r
+\r
+<p>The example above defines two environment variables with names\r
+MAFFT-BINARIES and FASTA_4_MAFFT and values /homes/cengine/mafft\r
+and /bin/fasta34 respectively. Semicolon is used as a separator\r
+between different environment variables whereas hash is used as a\r
+separator for name and value of the variable.</p>\r
+\r
+<h4><a name="mafftconf" id="mafftconf"></a>Configure JABAWS to Work\r
+with Mafft</h4>\r
+\r
+<p>If you use default configuration you do not need to read any\r
+further. The default configuration will work for you without any\r
+changes, however, if you want to install Mafft yourself then there\r
+is a couple of more steps to do.</p>\r
+\r
+<p>Mafft executable needs to know the location of other files\r
+supplied with Mafft. In addition some Mafft functions depends on\r
+the fasta executable, which is not supplied with Mafft, but is a\r
+separate package. Mafft needs to know the location of fasta34\r
+executable.</p>\r
+\r
+<p>To let Mafft know where the other files from its package are\r
+change the value of MAFFT-BINARIES environment variables. To let\r
+Mafft know where is the fasta34 executable set the value of\r
+FASTA_4_MAFFT environment variable to point to a location of\r
+fasta34 program. The latter can be added to the PATH variable\r
+instead. If you are using executables supplied with JABAWS, the\r
+path to Mafft binaries would be like <span class=\r
+"hightlight"><relative path to web application\r
+directory>/binaries/src/mafft/binaries</span> and the path to\r
+fasta34 binary would be <span class="hightlight"><relative path\r
+to web application\r
+directory>/binaries/src/fasta34/fasta34</span>. You can specify\r
+the location of Mafft binaries as well as fasta34 program elsewhere\r
+by providing an absolute path to them. All these settings are\r
+defined in <span class=\r
+"hightlight">conf/Executable.properties</span> file.</p>\r
+\r
<h4>Testing JABA Web Services</h4>\r
-<p>You can use a command line client (part of the client only package) to test you JABAWS installation as described <a href="howto.html#usingcclient">here</a>. If you downloaded a JABAWS server package, you can use <span class="hightlight"><your_jaba_context_name>/WEB-INF/lib/jaba-client.jar</span> to test JABAWS installation as described in <a href="howto.html#usingWsTester">how-to</a>. If you downloaded the source code, then you could run a number of test suits defined in the build.xml ant build file. </p>\r
-\r
-<h4><a name="logfiles" id="logfiles"></a>JABAWS Log Files </h4>\r
-<p>JABAWS can be configured to log what it is doing. This comes handy if you would like to see who is using your web services or need to chase some problems. JABAWS uses <a href="http://logging.apache.org/log4j/1.2/">log4j</a> to do the logging, the example of log4j configuration is bundled with JABAWS war file. You will find it in the <span class="hightlight">/WEB-INF/classes/log4j.properties</span> file. All the lines in this file are commented out. The reason why the logging is disabled by default it simple, log4j have to know the exact location where the log files should be stored. This is not known up until the deployment time. To enable the logging you need to define <span class="hightlight">logDir </span>property in the <span class="hightlight">log4j.properties</span> and uncomment section of the file which corresponds to your need. More information is given in the <span class="hightlight">log4j.properties</span> file itself. Restart the tomcat or the JABAWS web application to apply the settings. </p>\r
-<p>After you have done this, assuming that you did not change the log4j.properties file yourself, you should see the application log file called <span class="hightlight">activity.log</span>. The amount of information logged can be adjusted using different logging levels, it is reduced in the following order of log levels TRACE, DEBUG, INFO, WARN, ERROR, FATAL. </p>\r
-<p>If you would like to know who is using your services, you might want to <a href="howto.html#logs">enable tomcat access logging</a>. </p>\r
-<h4><a name="warfile" id="warfile"></a>JABAWS War File Content </h4>\r
-<table width="100%" >\r
- <tr>\r
- <th width="19%">Directory</th>\r
- <th width="81%">Content description </th>\r
- </tr>\r
- <tr>\r
- <td>conf/</td>\r
- <td> contains configuration files such as Executable.properties, Engine.local.properties, Engine.cluster.properties</td>\r
- </tr>\r
- <tr>\r
- <td>conf/settings</td>\r
- <td>Contains individual executable description files. In particular XXXParameters.xml, XXXPresets.xml, XXXLimits.xml where XXX is the name of the executable </td>\r
- </tr>\r
- <tr>\r
- <td>jobsout/</td>\r
- <td>Individual executables input, output and some other task related files are stored. (optional) </td>\r
- </tr>\r
- <tr>\r
- <td>binaries/</td>\r
- <td>Directory contains native executables - alignment programs, windows binaries (optional) </td>\r
- </tr>\r
- <tr>\r
- <td>binaries/src</td>\r
- <td>Contains source of native executables and Linux i386 binaries. </td>\r
- </tr>\r
- <tr>\r
- <td>binaries/matrices</td>\r
- <td>Substitution matrices</td>\r
- </tr>\r
- <tr>\r
- <td>WEB-INF</td>\r
- <td>Web application descriptor </td>\r
- </tr>\r
- <tr>\r
- <td>WEB-INF/lib</td>\r
- <td>Web application libraries </td>\r
- </tr>\r
- <tr>\r
- <td>WEB-INF/classes</td>\r
- <td>log4j.properties - log configuration file (optional) </td>\r
- </tr>\r
- <tr>\r
- <td colspan="2"><strong>Help Pages </strong></td>\r
- </tr>\r
- <tr>\r
- <td>/</td>\r
- <td> help pages, index.html is the starting page</td>\r
- </tr>\r
- <tr>\r
- <td>dm_javadoc</td>\r
- <td>javadoc for JABAWS client (the link is available from How To pages) </td>\r
- </tr>\r
- <tr>\r
- <td>prog_docs</td>\r
- <td>documentation for programmes that JABAWS uses </td>\r
- </tr>\r
- <tr>\r
- <td>images</td>\r
- <td>images referenced by html pages</td>\r
- </tr>\r
+\r
+<p>You can use a command line client (part of the client only\r
+package) to test you JABAWS installation as described <a href=\r
+"howto.html#usingcclient">here</a>. If you downloaded a JABAWS\r
+server package, you can use <span class=\r
+"hightlight"><your_jaba_context_name>/WEB-INF/lib/jaba-client.jar</span>\r
+to test JABAWS installation as described in <a href=\r
+"howto.html#usingWsTester">how-to</a>. If you downloaded the source\r
+code, then you could run a number of test suits defined in the\r
+build.xml ant build file.</p>\r
+\r
+<h4><a name="logfiles" id="logfiles"></a>JABAWS Log Files</h4>\r
+\r
+<p>JABAWS can be configured to log what it is doing. This comes\r
+handy if you would like to see who is using your web services or\r
+need to chase some problems. JABAWS uses <a href=\r
+"http://logging.apache.org/log4j/1.2/">log4j</a> to do the logging,\r
+the example of log4j configuration is bundled with JABAWS war file.\r
+You will find it in the <span class=\r
+"hightlight">/WEB-INF/classes/log4j.properties</span> file. All the\r
+lines in this file are commented out. The reason why the logging is\r
+disabled by default it simple, log4j have to know the exact\r
+location where the log files should be stored. This is not known up\r
+until the deployment time. To enable the logging you need to\r
+define<span class="hightlight">logDir</span> property in the <span\r
+class="hightlight">log4j.properties</span> and uncomment section of\r
+the file which corresponds to your need. More information is given\r
+in the <span class="hightlight">log4j.properties</span> file\r
+itself. Restart the tomcat or the JABAWS web application to apply\r
+the settings.</p>\r
+\r
+<p>After you have done this, assuming that you did not change the\r
+log4j.properties file yourself, you should see the application log\r
+file called <span class="hightlight">activity.log</span>. The\r
+amount of information logged can be adjusted using different\r
+logging levels, it is reduced in the following order of log levels\r
+TRACE, DEBUG, INFO, WARN, ERROR, FATAL.</p>\r
+\r
+<p>If you would like to know who is using your services, you might\r
+want to <a href="howto.html#logs">enable tomcat access\r
+logging</a>.</p>\r
+\r
+<h4><a name="warfile" id="warfile"></a>JABAWS War File Content</h4>\r
+\r
+<table width="100%">\r
+<tr>\r
+<th width="19%">Directory</th>\r
+<th width="81%">Content description</th>\r
+</tr>\r
+\r
+<tr>\r
+<td>conf/</td>\r
+<td>contains configuration files such as Executable.properties,\r
+Engine.local.properties, Engine.cluster.properties</td>\r
+</tr>\r
+\r
+<tr>\r
+<td>conf/settings</td>\r
+<td>Contains individual executable description files. In particular\r
+XXXParameters.xml, XXXPresets.xml, XXXLimits.xml where XXX is the\r
+name of the executable</td>\r
+</tr>\r
+\r
+<tr>\r
+<td>jobsout/</td>\r
+<td>Contains directories generated when running an individual executable. E.g. input and output files and some other task\r
+related data. (optional)</td>\r
+</tr>\r
+\r
+<tr>\r
+<td>binaries/</td>\r
+<td>Directory contains native executables - programs,\r
+windows binaries (optional)</td>\r
+</tr>\r
+\r
+<tr>\r
+<td>binaries/src</td>\r
+<td>Contains source of native executables and Linux i386\r
+binaries.</td>\r
+</tr>\r
+\r
+<tr>\r
+<td>binaries/matrices</td>\r
+<td>Substitution matrices <!-- what format ? --></td>\r
+</tr>\r
+\r
+<tr>\r
+<td>WEB-INF</td>\r
+<td>Web application descriptor</td>\r
+</tr>\r
+\r
+<tr>\r
+<td>WEB-INF/lib</td>\r
+<td>Web application libraries</td>\r
+</tr>\r
+\r
+<tr>\r
+<td>WEB-INF/classes</td>\r
+<td>log4j.properties - log configuration file (optional)</td>\r
+</tr>\r
+\r
+<tr>\r
+<td colspan="2"><strong>Help Pages</strong> </td>\r
+</tr>\r
+\r
+<tr>\r
+<td>/</td>\r
+<td>help pages, index.html is the starting page</td>\r
+</tr>\r
+\r
+<tr>\r
+<td>dm_javadoc</td>\r
+<td>javadoc for JABAWS client (the link is available from How To\r
+pages)</td>\r
+</tr>\r
+\r
+<tr>\r
+<td>prog_docs</td>\r
+<td>documentation for programmes that JABAWS uses</td>\r
+</tr>\r
+\r
+<tr>\r
+<td>images</td>\r
+<td>images referenced by html pages</td>\r
+</tr>\r
</table>\r
+\r
<p> </p>\r
</div>\r
-<!-- content end--> \r
-<div id="copyright">Last update: 7 July 2010<br/>\r
-Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
-</div><!-- wrapper end-->\r
-</div> <!-- page end-->\r
\r
+<!-- content end-->\r
+<div id="copyright">Last update: 19 August 2010<br />\r
+ Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
+Dundee, UK</div>\r
+</div>\r
+\r
+<!-- wrapper end-->\r
+</div>\r
+<!-- page end-->\r
+\r
+<!-- Google analitics -->\r
+<script type="text/javascript">\r
+var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");\r
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+</script>\r
+<script type="text/javascript">\r
+try{\r
+var pageTracker = _gat._getTracker("UA-5356328-1");\r
+pageTracker._trackPageview();\r
+} catch(err) {}\r
+</script>\r
</body>\r
</html>\r
\r
border: 1px dashed black;\r
}\r
\r
+\r
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- font-size-adjust:0.4;\r
+ font-size-adjust:0.5;\r
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+ font-family:Arial, Helvetica, sans-serif;\r
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<div id="banner">\r
-<h2><span class="headeru">JA</span>va <span class="headeru">B</span>ioinformatics <span class="headeru">A</span>nalyses <span class="headeru">W</span>eb <span class="headeru">S</span>ervices</h2>\r
+<table> \r
+<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img class="logo" src="images/uod_lt.gif" alt="University of Dundee" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><h2><span class="headeru">JA</span>va <span class=\r
+"headeru">B</span>ioinformatics <span class="headeru">A</span>nalysis <span class="headeru">W</span>eb <span\r
+class="headeru">S</span>ervices</h2></td>\r
+</tr>\r
+</table>\r
</div><!-- banner end-->\r
+\r
<div id="wrapper">\r
<div id="panel">\r
<p><a href="index.html">Home</a>\r
<a href="howto.html">How To</a>\r
<a href="download.html">Download</a>\r
<a class="selected" href="develhome.html">For Developers</a>\r
+ <a href="http://www.compbio.dundee.ac.uk">Barton Group</a> \r
<a href="http://www.jalview.org">Jalview</a> </p>\r
</div>\r
<!-- panel end-->\r
\r
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- background-position:left bottom;\r
- background-image:url("images/banner_bg.gif");\r
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- 0.1em 0.1em 0.05em black \r
- */\r
-}\r
+#banner { background-color:white; }\r
\r
+/*\r
+See index.html banner commented out code for an example of use \r
+.uniicon { overflow: hidden; display:inline; padding:0; margin:0; float:right; position:relative; top:1em; } \r
+.uniicon a img {border:none;} \r
+*/\r
#panel { width:150px; background:url("images/panel_bg.gif") repeat-y ; float:left;\r
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}\r
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\r
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+#wrapper { background:url("images/panel_bg.gif") repeat-y left top; }\r
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+ font-family:Arial, Helvetica, sans-serif;\r
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+ font-size:0.9em;\r
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border: 1px solid black;\r
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\r
/* Table styles */\r
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+\r
+\r
+#wrapper table {\r
border-collapse: collapse; \r
border: 1px solid #666;\r
margin: 20px 0 20px 0;\r
width: 100%;\r
}\r
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+#wrapper th, #wrapper td {\r
margin: 2px 4px 2px 4px;\r
padding: 0 5px;\r
text-align: left;\r
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+#wrapper table caption {\r
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- background-color: #9c9;\r
- text-align:center;\r
- line-height:1em;\r
-}\r
\r
-tr {\r
+#wrapper tr {\r
background-color: #eee; \r
}\r
\r
-tr:nth-child(odd) {\r
+#wrapper tr:nth-child(odd) {\r
background-color: #ccc; \r
}\r
\r
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- margin: 1em;\r
font-family:Arial, Helvetica, sans-serif;\r
font-size: 9pt;\r
background-color: white;\r
line-height: 2em;\r
+ min-width:35em;\r
}\r
+\r
+\r
+#banner table {\r
+ border-collapse: collapse; \r
+ border: none;\r
+ padding:0;\r
+ margin:0;\r
+ color:white;\r
+ text-align:center;\r
+ vertical-align:middle;\r
+ line-height:1.5em;\r
+ width: 100%;\r
+}\r
+\r
+#banner td.bg {\r
+ border-collapse: collapse; \r
+ background-image:url("images/banner_bg.gif");\r
+ background-repeat: repeat-x; \r
+ background-color:transparent;\r
+ background-position:inherit;\r
+}\r
+\r
+img.logo {\r
+ border-top:1px solid #003b62; \r
+ border-left:1px solid #003b62; \r
+ border-right:none; \r
+ border-bottom: none; \r
+ margin:0; \r
+ padding:0; \r
+ display:inline\r
+}
\ No newline at end of file
git://source.jalview.org / jabaws.git / commitdiff
