Executable.properties

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JWS-112 Hotfix the last t-coffee version 11. The -mode quickaln preset breaks if ’t_coffee’ is not found in $PATH. By calling t_coffee.sh instead, the problem is fixed by updating the $PATH on the flight and passing the original arguments to t_coffee.

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JWS-112 Updated AACon to version 1.1.

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JWS-114 Fixed the paths to the cluster executables.

Updated configs for testing local/cluster mode in the internal webservices2 boxe.

  1. … 7 more files in changeset.
JWS-114 Commented out ‘cluster’ entries for consistency with other methods.

JWS-113 Commented Jpred entries in various configuration files.

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Define path to UNIREF database in conf/Executable.properties

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Add all needed infrastructure for MSAprobs and GLprobs

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Add lost description of RNAalifold from ViennaRNA

merged conf/Executable.properties

Parameter bug fixed, Jalview will now run some parameters

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JWS-71 - nominal Limits for RNAFold service - necessary so 'drmaa library not found' exception isn't raised when submitting to cluster

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Clean-up, refactoring, commenting. Parameters file containts only options since Jalview still can't deal with them

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conf/Executable.properties and compilebin.sh updated for linux.

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Webservice which implements FoldWS and returns String. Parameters.xml file updated in line with the RunnerConfig schema.

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uncomment limit files in order to make some tests successful

Basic Testing Setup, no getResults method yet

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Re-format configuration files

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JWS-67 Add Jpred to configuration files

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RNAalifold.java runner and RNAalifoldTester incomplete

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Website files updated for JABAWS 3.0a

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JWS-27 replaced JRonn with patched biojava 3.0.4 version which runs correctly for large sets of sequences in multithreaded mode

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Minor changes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4526 e3abac25-378b-4346-85de-24260fe3988d

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Get rid of v_hmem settings

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4474 e3abac25-378b-4346-85de-24260fe3988d

ClustalO settings

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4467 e3abac25-378b-4346-85de-24260fe3988d

  1. … 3 more files in changeset.
Wrapper for Clustal Omega.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4458 e3abac25-378b-4346-85de-24260fe3988d

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formatting change

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4396 e3abac25-378b-4346-85de-24260fe3988d

Pre release Executable.properties, help added, unused properties commented out

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4393 e3abac25-378b-4346-85de-24260fe3988d

Better method for searching JAVA

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4392 e3abac25-378b-4346-85de-24260fe3988d

  1. … 3 more files in changeset.
obtain JAVA executable path from the JAVA_HOME variable. Does not require path to java for jar libraries.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4376 e3abac25-378b-4346-85de-24260fe3988d

  1. … 3 more files in changeset.