1 ###########################################################################################
3 # THIS IS JABAWS EXECUTABLE CONFIGURATION FILE FOR DUNDEE #
5 ###########################################################################################
7 ### Properties supported by executables.
8 ### <execname> is one of the available applications:
9 ### [clustalw, mafft, muscle, propcons, tcoffee, iupred, jronn, globplot, disembl, aacon, jpred]
11 ### Path to the native executable on Windows must be either absolute,
12 ### or relative to JABAWS web application
13 # local.<execname>.bin.windows = binaries/windows/clustalw2.exe
15 ### Path to the native executable not on Windows (e.g. Linux, Mac)
16 ### must be either absolute, or relative to JABAWS web application
17 # local.<execname>.bin = binaries/src/clustalw/src/clustalw2
19 ### Path to the native executable on the Cluster (must be accessible from all
20 ### Cluster nodes which will run JABAWS jobs). The path must be absolute.
21 # cluster.<execname>.bin = /home/jabaws/binaries/src/clustalw/src/clustalw2
23 ### At least one of the path to the native executable should be defined.
25 ### If an application supports presets, the preset file can have either
26 ### absolute or relative to the JABAWS web application path to the file.
27 ### The file is optional.
28 # <execname>.presets.file = conf/settings/ClustalPresets.xml
30 ### If an application supports parameters, the parameter file can have either
31 ### absolute or relative to the JABAWS web application path to the file.
32 ### The file is optional.
33 # <execname>.parameters.file = conf/settings/ClustalParameters.xml
35 ## Application limits, absolute or relative to
36 ## the JABAWS web application path to the file. Optional.
37 ## Use this if you want to limit the size of the job to be accepted by a
38 ## Webservice. The limits files we use in Dundee are provided with JABAWS.
39 # <execname>.limits.file=conf/settings/ClustalLimits.xml
41 ## Flags passed to the Cluster batch manager for the application. Optional.
42 ## This example sets a maximum execution time to 24 hours and maximum amount of
43 ## memory per task to 6Gb for SGE and OGE Cluster batch managers.
44 ## Please note that all the examples of this parameter below are correct for
45 ## Sun Grid Engine or Open Grid Engine (untested) only! If you use a different
46 ## batch manager you would need to specify different flags.
47 # <execname>.cluster.settings = -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
49 ## Environmental variables required by native executables. Optional.
50 ## Format: VARIABLE_NAME1#VARIABLE_VALUE1;VARIABLE_NAME2#VARIABLE_VALUE2;
51 # <execname>.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;
53 ## Parameter supported by the executable Jar files, such as jronn and aacon,
54 ## point to the location of the jar file. Also, local.<execname>.bin,
55 ## local.<execname>.bin.windows properties are optional for these, if not
56 ## provided they will be replaced to the java executable path from JAVA_HOME
57 ## environmental variable.
58 #<execname>.jar.file = binaries/windows/bj3.0.4p-jronn.jar
60 ###########################################################################################
61 # CLUSTAL W CONFIGURATION #
62 ###########################################################################################
63 local.clustalw.bin.windows = binaries/windows/clustalw2.exe
64 local.clustalw.bin = binaries/src/clustalw/src/clustalw2
65 cluster.clustalw.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/clustalw/src/clustalw2
66 ### This parameters specifies the directory where the matrices files are stored
67 clustalw.-matrix.path = binaries/matrices
68 clustalw.presets.file = conf/settings/ClustalPresets.xml
69 clustalw.parameters.file = conf/settings/ClustalParameters.xml
70 clustalw.limits.file = conf/settings/ClustalLimits.xml
71 clustalw.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
74 ###########################################################################################
75 # CLUSTAL OMEGA CONFIGURATION #
76 ###########################################################################################
77 local.clustalo.bin.windows = binaries/windows/clustalo/clustalo.exe
78 local.clustalo.bin = binaries/src/clustalo/src/clustalo
79 cluster.clustalo.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/clustalo/src/clustalo
80 ### This parameters specifies the directory where the matrices files are stored
81 #clustalo.presets.file = conf/settings/ClustaloPresets.xml
82 clustalo.parameters.file = conf/settings/ClustaloParameters.xml
83 clustalo.limits.file = conf/settings/ClustaloLimits.xml
84 ### ClustalO can be executed on multiple CPUs. This parameter specifies the number of CPUs:
85 clustalo.cluster.cpunum = 4
86 ### This reserves a slot with CPUNUM on the Cluster for the task
87 clustalo.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M
90 ###########################################################################################
91 # MUSCLE CONFIGURATION #
92 ###########################################################################################
93 local.muscle.bin.windows = binaries/windows/muscle.exe
94 local.muscle.bin = binaries/src/muscle/muscle
95 cluster.muscle.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/muscle/muscle
96 ### This parameters specifies the directory where the matrices files are stored
97 muscle.-matrix.path = binaries/matrices
98 muscle.presets.file = conf/settings/MusclePresets.xml
99 muscle.parameters.file = conf/settings/MuscleParameters.xml
100 muscle.limits.file = conf/settings/MuscleLimits.xml
101 muscle.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
104 ###########################################################################################
105 # MAFFT CONFIGURATION #
106 ###########################################################################################
107 local.mafft.bin = binaries/src/mafft/scripts/mafft
108 cluster.mafft.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/mafft/scripts/mafft
109 # These paths will be converted to absolute if relative.
110 mafft.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;
111 ### This parameters specifies the directory where the matrices files are stored
112 mafft.--aamatrix.path = binaries/matrices
113 mafft.presets.file = conf/settings/MafftPresets.xml
114 mafft.parameters.file = conf/settings/MafftParameters.xml
115 mafft.limits.file = conf/settings/MafftLimits.xml
116 mafft.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
119 ###########################################################################################
120 # TCOFFEE CONFIGURATION #
121 ###########################################################################################
122 local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee.sh
123 cluster.tcoffee.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee.sh
124 # This variable is required by tcoffee
125 tcoffee.bin.env = HOME_4_TCOFFEE#jobsout;
126 tcoffee.presets.file = conf/settings/TcoffeePresets.xml
127 tcoffee.parameters.file = conf/settings/TcoffeeParameters.xml
128 tcoffee.limits.file = conf/settings/TcoffeeLimits.xml
129 ### Tcoffee can be executed on multiple CPUs. This parameter specifies the number of CPUs:
130 tcoffee.cluster.cpunum = 4
131 ### This reserves a slot with CPUNUM on the Cluster for the task
132 tcoffee.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M
135 ###########################################################################################
136 # PROBCONS CONFIGURATION #
137 ###########################################################################################
138 local.probcons.bin = binaries/src/probcons/probcons
139 cluster.probcons.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/probcons/probcons
140 probcons.parameters.file = conf/settings/ProbconsParameters.xml
141 probcons.limits.file = conf/settings/ProbconsLimits.xml
142 probcons.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
145 ###########################################################################################
146 # JRONN CONFIGURATION #
147 ###########################################################################################
148 ### If no local path is specified, Java is loaded from JAVA_HOME variable for local execution
149 ### However, cluster.jronn.bin MUST be specified for running Jronn on the Cluster.
150 #local.jronn.bin.windows = D:\\Java\\jdk1.6.0_24\\bin\\java.exe
151 local.jronn.bin = /homes/www-jws2/java/jdk/bin/java
152 cluster.jronn.bin = /homes/www-jws2/java/jdk/bin/java
153 jronn.jar.file = binaries/windows/bj3.0.4p-jronn.jar
154 jronn.limits.file = conf/settings/JronnLimits.xml
155 ### Jronn can use multiple CPUs. This parameter specifies the number of CPU:
156 jronn.cluster.cpunum = 4
157 ### This reserves a slot with CPUNUM on the Cluster for the task
158 jronn.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=6000M
161 ###########################################################################################
162 # DISEMBL CONFIGURATION #
163 ###########################################################################################
164 local.disembl.bin = binaries/src/disembl/DisEMBL.py
165 cluster.disembl.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/disembl/DisEMBL.py
166 disembl.limits.file = conf/settings/DisemblLimits.xml
167 disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
170 ###########################################################################################
171 # GLOBPLOT CONFIGURATION #
172 ###########################################################################################
173 local.globplot.bin = binaries/src/globplot/GlobPlot.py
174 cluster.globplot.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/globplot/GlobPlot.py
175 globplot.bin.env = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/globplot/biopython-1.50
176 globplot.limits.file = conf/settings/GlobPlotLimits.xml
177 globplot.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
180 ###########################################################################################
181 # IUPRED CONFIGURATION #
182 ###########################################################################################
183 #local.iupred.bin.windows = binaries/windows/iupred/iupred.exe
184 local.iupred.bin = binaries/src/iupred/iupred
185 ### This must point to the directory where iupred binary is, with other files it
186 ### depends on. This path will be converted to absolute if relative at runtime.
187 iupred.bin.env = IUPred_PATH#binaries/src/iupred
188 cluster.iupred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/iupred/iupred
189 iupred.parameters.file = conf/settings/IUPredParameters.xml
190 iupred.limits.file = conf/settings/IUPredLimits.xml
191 iupred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
194 ###########################################################################################
195 # AACON CONFIGURATION #
196 ###########################################################################################
197 ### This is just a path to the standard java executable
198 local.aacon.bin = /homes/www-jws2/java/jdk/bin/java
199 cluster.aacon.bin = /homes/www-jws2/java/jdk/bin/java
200 ### Path to the AACon library
201 aacon.jar.file = binaries/windows/compbio-conservation-1.1.jar
202 aacon.parameters.file = conf/settings/AAConParameters.xml
203 aacon.presets.file = conf/settings/AAConPresets.xml
204 aacon.limits.file = conf/settings/AAConLimits.xml
205 ### AACon can use multiple CPUs
206 ### This parameter specifies the number of CPUs to use
207 aacon.cluster.cpunum = 4
208 ### This reserves a slot with CPUNUM on the Cluster for the task
209 aacon.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M
211 ###########################################################################################
212 # JPRED CONFIGURATION #
213 ###########################################################################################
214 #local.jpred.bin = binaries/src/jpred/jpred.pl
215 #cluster.jpred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/jpred/jpred.pl
216 ## These paths will be converted to absolute if relative.
217 #jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast
218 ## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If
219 ## you install the database to a different path chenge the variable here
220 #jpred.data.uniref.path = /homes/www-jpred/databases
222 ## Redefine jpred.data.uniref.name if you do undestand what the variable means
223 #jpred.data.uniref.name = cluster
224 #### This parameters specifies the directory where the matrices files are stored
225 #jpred.presets.file = conf/settings/JpredPresets.xml
226 #jpred.parameters.file = conf/settings/JpredParameters.xml
227 #jpred.limits.file = conf/settings/JpredLimits.xml
228 #jpred.cluster.cpunum = 4
229 #jpred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=8000M
231 ###########################################################################################
232 # RNAALIFOLD CONFIGURATION #
233 ###########################################################################################
234 local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe
235 local.rnaalifold.bin = binaries/src/ViennaRNA/Progs/RNAalifold
236 cluster.rnaalifold.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/ViennaRNA/Progs/RNAalifold
237 rnaalifold.parameters.file = conf/settings/RNAalifoldParameters.xml
238 rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml
239 rnaalifold.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
241 ###########################################################################################
242 # MSAProbs CONFIGURATION #
243 ###########################################################################################
244 local.msaprobs.bin = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs
245 cluster.msaprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs
246 msaprobs.parameters.file = conf/settings/MSAprobsParameters.xml
247 msaprobs.limits.file = conf/settings/MSAprobsLimits.xml
248 msaprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M
250 ###########################################################################################
251 # GLprobs CONFIGURATION #
252 ###########################################################################################
253 local.glprobs.bin = binaries/src/GLProbs-1.0/glprobs
254 cluster.glprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/GLProbs-1.0/glprobs
255 glprobs.parameters.file = conf/settings/GLprobsParameters.xml
256 glprobs.limits.file = conf/settings/GLprobsLimits.xml
257 glprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M