jabaws

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JWS-114 Bumping varied config files and jetbrains xmls. Also adding some java classes that are generated during the compilation.

    • binary
    /ExecutionStatistic/log/log11.dat
    • binary
    /WEB-INF/classes/lib/testng-5.10-jdk15.jar
    • -0
    • +51
    /WEB-INF/classes/log4j.properties.dundee
    • -0
    • +62
    /WEB-INF/classes/log4j.properties.full
    • -0
    • +27
    /WEB-INF/classes/log4j.properties.statdb
    • -0
    • +417
    /engine/compbio/engine/client/Util.java
    • -0
    • +100
    /engine/compbio/engine/cluster/drmaa/AsyncJobRunner.java
    • -0
    • +95
    /engine/compbio/engine/cluster/drmaa/ClusterUtil.java
    • -0
    • +395
    /engine/compbio/engine/cluster/drmaa/JobRunner.java
    • -0
    • +134
    /runner/compbio/runner/Util.java
JWS-116 Added entries for the jabaws docs source files to the build.xml

JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.

    • binary
    /binaries/src/GLProbs-1.0/MSA.o
    • binary
    /binaries/src/GLProbs-1.0/MSAClusterTree.o
    • binary
    /binaries/src/GLProbs-1.0/MSAGuideTree.o
    • binary
    /binaries/src/GLProbs-1.0/MSAPartProbs.o
    • binary
    /binaries/src/GLProbs-1.0/MSAReadMatrix.o
    • binary
    /binaries/src/GLProbs-1.0/main.o
    • binary
    /binaries/src/MSAProbs-0.9.7/MSAProbs/MSA.o
    • binary
    /binaries/src/MSAProbs-0.9.7/MSAProbs/MSAClusterTree.o
    • binary
    /binaries/src/MSAProbs-0.9.7/MSAProbs/MSAReadMatrix.o
    • binary
    /binaries/src/MSAProbs-0.9.7/MSAProbs/main.o
    • -0
    • +523
    /binaries/src/ViennaRNA/H/Makefile
  1. … 1787 more files in changeset.
JWS-109 Fixed the links in the navbar header and footer to match the new documentation pages.

JWS-109 General improvements and further fixes to typos and proofreading.

JWS-116 Moved the boostrap’ed manual pages to a temporary dir. The documentation pages are now generated with Sphinx.

    • -0
    • +306
    /website/man_pages_old/man_about.jsp
    • -0
    • +155
    /website/man_pages_old/man_client.jsp
    • -0
    • +660
    /website/man_pages_old/man_configuration.jsp
    • -0
    • +561
    /website/man_pages_old/man_dev.jsp
    • -0
    • +160
    /website/man_pages_old/man_docs.jsp
    • -0
    • +431
    /website/man_pages_old/man_server_dev.jsp
    • -0
    • +271
    /website/man_pages_old/man_servervm.jsp
    • -0
    • +495
    /website/man_pages_old/man_serverwar.jsp
    • -0
    • +330
    /website/man_pages_old/man_stats.jsp
  1. … 4 more files in changeset.
JWS-116 Added the Sphinx generated documentation pages to website/docs.

    • binary
    /website/docs/_images/VMware_booted.png
    • binary
    /website/docs/_images/VMware_cpu.png
    • binary
    /website/docs/_images/folder-small.png
    • binary
    /website/docs/_images/usage_statistics_details.gif
    • binary
    /website/docs/_images/usage_statistics_job_details.gif
    • binary
    /website/docs/_images/usage_statistics_main.gif
    • binary
    /website/docs/_images/usage_statistics_month.gif
    • binary
    /website/docs/_images/vm_welcome_screen.png
    • binary
    /website/docs/_images/ws-structure.png
    • -0
    • +473
    /website/docs/_sources/advanced.rst.txt
    • -0
    • +90
    /website/docs/_sources/changelog.rst.txt
    • -0
    • +11
    /website/docs/_sources/citations.rst.txt
    • -0
    • +118
    /website/docs/_sources/client.rst.txt
    • -0
    • +635
    /website/docs/_sources/develop.rst.txt
    • -0
    • +160
    /website/docs/_sources/getting_started.rst.txt
  1. … 68 more files in changeset.
JWS-116 Added a full set of manual pages in reStructuredText format that are built with Sphinx.

    • -0
    • +15
    /docs/_themes/sphinx_rtd_theme/__init__.py
    • -0
    • +51
    /docs/_themes/sphinx_rtd_theme/footer.html
    • -0
    • +214
    /docs/_themes/sphinx_rtd_theme/layout.html
    • -0
    • +209
    /docs/_themes/sphinx_rtd_theme/layout_old.html
    • -0
    • +50
    /docs/_themes/sphinx_rtd_theme/search.html
    • -0
    • +9
    /docs/_themes/sphinx_rtd_theme/searchbox.html
    • -0
    • +5
    /docs/_themes/sphinx_rtd_theme/static/css/theme.css
  1. … 28 more files in changeset.
JWS-114 Fixed the paths to the cluster executables.

JWS-114 Added two extra test sets for testing web_services and running all tests.

JWS-114 Set JAVA_TARGET as a property and fixed the LIBRARY_PATH

JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.

    • -0
    • +203
    /binaries/src/tcoffee/example/1D4V-1.pdb
    • -0
    • +340
    /binaries/src/tcoffee/example/1D4V-2.pdb
    • -0
    • +325
    /binaries/src/tcoffee/example/1D4V-3.pdb
    • -0
    • +300
    /binaries/src/tcoffee/example/1EXT-1.pdb
    • -0
    • +329
    /binaries/src/tcoffee/example/1EXT-2.pdb
    • -0
    • +343
    /binaries/src/tcoffee/example/1EXT-3.pdb
    • -0
    • +229
    /binaries/src/tcoffee/example/1EXT-4.pdb
    • -0
    • +257
    /binaries/src/tcoffee/example/1JMA-1.pdb
    • -0
    • +318
    /binaries/src/tcoffee/example/1JMA-2.pdb
    • -0
    • +234
    /binaries/src/tcoffee/example/1OQE-1.pdb
    • -0
    • +240
    /binaries/src/tcoffee/example/1SG1-1.pdb
    • -0
    • +307
    /binaries/src/tcoffee/example/1SG1-2.pdb
    • -0
    • +303
    /binaries/src/tcoffee/example/1SG1-3.pdb
  1. … 457 more files in changeset.
JWS-112 Bumping version of Mafft to version 7.310.

    • binary
    /binaries/src/mafft/binaries/addsingle
    • binary
    /binaries/src/mafft/binaries/contrafoldwrap
    • binary
    /binaries/src/mafft/binaries/countlen
    • binary
    /binaries/src/mafft/binaries/disttbfast
    • binary
    /binaries/src/mafft/binaries/dndblast
    • binary
    /binaries/src/mafft/binaries/dndfast7
    • binary
    /binaries/src/mafft/binaries/dndpre
    • binary
    /binaries/src/mafft/binaries/dvtditr
    • binary
    /binaries/src/mafft/binaries/getlag
    • binary
    /binaries/src/mafft/binaries/mafft-distance
    • binary
    /binaries/src/mafft/binaries/mafft-profile
    • binary
    /binaries/src/mafft/binaries/makedirectionlist
  1. … 199 more files in changeset.
JWS-112 Bumping version of ClustalW (src, binaries and windows) to version 2.1.

    • -0
    • +165
    /binaries/src/clustalw/COPYING.LESSER
    • -77
    • +156
    /binaries/src/clustalw/Makefile
    • -62
    • +141
    /binaries/src/clustalw/Makefile.in
    • -61
    • +133
    /binaries/src/clustalw/aclocal.m4
    • -50
    • +57
    /binaries/src/clustalw/config.guess
    • -0
    • +643
    /binaries/src/clustalw/config.log
    • -270
    • +257
    /binaries/src/clustalw/config.status
    • -16
    • +51
    /binaries/src/clustalw/config.sub
    • -2667
    • +1813
    /binaries/src/clustalw/configure
    • -36
    • +76
    /binaries/src/clustalw/m4/Makefile
  1. … 128 more files in changeset.
JWS-112 Bumping version of ClustalO (src, binaries and windows) to version 1.2.4.

    • -1
    • +106
    /binaries/src/clustalo/ChangeLog
    • -0
    • +706
    /binaries/src/clustalo/Makefile
    • -75
    • +218
    /binaries/src/clustalo/README
    • -0
    • +8
    /binaries/src/clustalo/_configs.sed
    • -0
    • +12
    /binaries/src/clustalo/clustalo.pc
    • -0
    • +2037
    /binaries/src/clustalo/config.log
    • -0
    • +2454
    /binaries/src/clustalo/config.status
    • -11
    • +11
    /binaries/src/clustalo/configure
    • -4
    • +25
    /binaries/src/clustalo/configure.ac
    • -185
    • +346
    /binaries/src/clustalo/depcomp
    • -202
    • +190
    /binaries/src/clustalo/install-sh
    • -0
    • +9062
    /binaries/src/clustalo/libtool
  1. … 316 more files in changeset.
Bumped the javac version.

Reverting to the absolute paths that actually exist and are available to other users in the cluster.

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

    • -110
    • +106
    /conf/Executable.properties
    • -74
    • +71
    /conf/Executable.properties.dundee
    • -10
    • +11
    /dundee-conf/Engine.cluster.properties
    • -130
    • +254
    /dundee-conf/Executable.properties
    • -0
    • +18
    /dundee-conf/GA.properties
Added new entries for ignoring .DS_Store and Thumbs.db

Updated the .idea xml configs. This should be ignored but since it is being tracked I decided to push the current changes.

    • -0
    • +14
    /.idea/deployment.xml
    • -0
    • +10
    /.idea/webServers.xml
JWS-109 Added a missing figure to the section descrbing the JABAWS codebase structure.

    • binary
    /website/static/img/ws-structure.png
JWS-109 Updated the Documentation pages. Fixed the links and fixed chuncks of text to improve readability.

JWS-109 & JWS-110 Updated the Downloads page so that it follows the same style as the getting started page.

JWS-109 & JWS-113 Improved the readability of the getting started guides. Also removed references to the installation of jpred dependencies.

JWS-109 Updated the home page. Made some changes to the text to improve readability.

JWS-109 Updated the base bootstrap theme header and footer. Also removed unused styling.

JWS-113 Commented Jpred entries in the datamodel, runner and webservices java source code.

    • -1
    • +1
    /datamodel/compbio/data/sequence/Program.java
    • -134
    • +134
    /runner/compbio/runner/predictors/Jpred.java
    • -1
    • +1
    /webservices/compbio/data/msa/Category.java
    • -16
    • +16
    /webservices/compbio/ws/client/Services.java
    • -5
    • +6
    /webservices/compbio/ws/client/WSTester.java
    • -151
    • +151
    /webservices/compbio/ws/server/JpredWS.java
    • -18
    • +18
    /webservices/compbio/ws/server/WSUtil.java
JWS-115 Bumping version to jabaws 2.2.

JWS-111 & JWS-109 Fixed some typos.

JWS-111 Fixed the location of the statspages, which are now included within the website folder.