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Tuesday 21 Jun 2011
6:17 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Fixes for failed test cases (most was due to the data being used or problems with test cases themselves)

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4303 e3abac25-378b-4346-85de-24260fe3988d

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    /binaries/src/clustalw/src/.deps/Alignment.Po
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    /binaries/src/clustalw/src/.deps/ClusterTree.Po
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    /binaries/src/clustalw/src/.deps/MSA.Po
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    /binaries/src/clustalw/src/.deps/Utility.Po
  16. … 10 more files in changeset.
4:44 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

custom test suit xml

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4302 e3abac25-378b-4346-85de-24260fe3988d

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    /temp-testng-customsuite.xml
3:48 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

tcoffee updated docs & todo

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4301 e3abac25-378b-4346-85de-24260fe3988d

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    /website/prog_docs/tcoffee.html
3:47 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

IA32 and x64 tcoffee binaries are added

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4300 e3abac25-378b-4346-85de-24260fe3988d

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3:34 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

getting rid of ambiguous documentation folder. all prog_doc are now stored in website/prog_docs

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4299 e3abac25-378b-4346-85de-24260fe3988d

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3:25 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

new version of tcoffee 8.99 not yet compiled for ia32 linux (currently compiled for dundee cluster)

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4298 e3abac25-378b-4346-85de-24260fe3988d

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  16. … 63 more files in changeset.
3:14 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

removing tcoffee to update

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4297 e3abac25-378b-4346-85de-24260fe3988d

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  16. … 57 more files in changeset.
1:29 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Revert multithreading support for mafft as it does not seem to work

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4296 e3abac25-378b-4346-85de-24260fe3988d

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    /runner/compbio/runner/msa/Mafft.java
1:29 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Revert multithreading support for mafft as it does not seem to work

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4295 e3abac25-378b-4346-85de-24260fe3988d

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1:06 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Get rind of NativeClusterJob interface as pretty much every jobs best to use some cluster settings, and they are simply defined in the executable conf file and passed by the SkeletalExecutable.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4294 e3abac25-378b-4346-85de-24260fe3988d

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    /runner/compbio/runner/msa/Tcoffee.java
12:35 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

mafft new location

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4293 e3abac25-378b-4346-85de-24260fe3988d

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    /conf/Executable.properties
12:34 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Changes to accomodate new version's of mafft packaging

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4292 e3abac25-378b-4346-85de-24260fe3988d

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12:33 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

add IA32 linux muscle binary

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4291 e3abac25-378b-4346-85de-24260fe3988d

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    /binaries/src/muscle/muscle
12:10 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

IA32 mafft executables

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4290 e3abac25-378b-4346-85de-24260fe3988d

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  16. … 19 more files in changeset.
11:58 am

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

New Mafft binaries for 32 bit linux system

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4289 e3abac25-378b-4346-85de-24260fe3988d

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  16. … 16 more files in changeset.
11:57 am

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

New Mafft binaries for 64 bit linux system

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4288 e3abac25-378b-4346-85de-24260fe3988d

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  16. … 16 more files in changeset.
11:27 am

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

remove mafft extensions - we do not support them

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4287 e3abac25-378b-4346-85de-24260fe3988d

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  16. … 34 more files in changeset.
11:02 am

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

new mafft v 6.857 with extensions

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4286 e3abac25-378b-4346-85de-24260fe3988d

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  16. … 143 more files in changeset.
11:01 am

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Removing old version of mafft to replace with the new

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4285 e3abac25-378b-4346-85de-24260fe3988d

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  16. … 238 more files in changeset.
Monday 20 Jun 2011
5:43 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

todo update

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4284 e3abac25-378b-4346-85de-24260fe3988d

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5:37 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

new version of muscle 3.8.31 binaries for various systems, sources, help file and configuration is updated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4283 e3abac25-378b-4346-85de-24260fe3988d

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    • -0
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    /binaries/src/muscle/glbalignns.cpp
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    /binaries/src/muscle/globals.cpp
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    /binaries/src/muscle/intmath.cpp
  16. … 35 more files in changeset.
Friday 17 Jun 2011
5:17 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

todos

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4282 e3abac25-378b-4346-85de-24260fe3988d

Options
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    /TODO.txt
4:45 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Web services refactoring & bug fixing

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4281 e3abac25-378b-4346-85de-24260fe3988d

Options
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    /webservices/compbio/ws/server/AAConWS.java
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    /webservices/compbio/ws/server/DisemblWS.java
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    /webservices/compbio/ws/server/JronnWS.java
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    /webservices/compbio/ws/server/MafftWS.java
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    /webservices/compbio/ws/server/_MsaService.java
3:06 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Refactoring of all SequenceAnnotation web services New version of Metro Definition for IUPred exec Stubs regenerated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4280 e3abac25-378b-4346-85de-24260fe3988d

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    • binary
    /WEB-INF/lib/webservices-tools.jar
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    /datamodel/compbio/data/sequence/FastaReader.java
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    /datamodel/compbio/data/sequence/SequenceUtil.java
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    /engine/compbio/engine/client/EnvVariableProcessor.java
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    /how_to_add_new_webservice.txt
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    /runner/compbio/runner/Util.java
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    /testsrc/compbio/ws/client/TestAAConWS.java
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    /webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
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  16. … 33 more files in changeset.
Thursday 16 Jun 2011
5:48 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

todos

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4279 e3abac25-378b-4346-85de-24260fe3988d

Options
    • -0
    • +1
    /TODO.txt
5:46 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Binaries relocation

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4278 e3abac25-378b-4346-85de-24260fe3988d

Options
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    /binaries/AACon_manual.txt
    • binary
    /binaries/aaconservation.jar
    • -720
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    /binaries/clustalw-help.txt
    • binary
    /binaries/clustalw2.exe
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    /binaries/help/clustalw-help.txt
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  16. … 12 more files in changeset.
5:18 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

IUPred for windows

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4277 e3abac25-378b-4346-85de-24260fe3988d

Options
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    /binaries/windows/iupred/ss_casp
3:40 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Integrating IUPredWS

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4276 e3abac25-378b-4346-85de-24260fe3988d

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    /wsbuild.xml
3:30 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

A few more tests for IUPred

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4275 e3abac25-378b-4346-85de-24260fe3988d

Options
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    /testsrc/compbio/runner/disorder/IUPredTester.java
3:22 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

IUPred final touches. All test cases pass

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4274 e3abac25-378b-4346-85de-24260fe3988d

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    /datamodel/compbio/data/sequence/ScoreManager.java
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    /runner/compbio/runner/disorder/IUPred.java
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