Previous changeset 28:a0c04d13a7cf (2013-06-12) Next changeset 30:061259d5e6e4 (2013-06-12) |
Commit message:
Uploaded |
modified:
rgedgeR/tool_dependencies.xml |
removed:
rgedgeR/test-data/gentestdata.sh~ rgedgeR/tool_dependencies.xml~ |
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diff -r a0c04d13a7cf -r 81255a103a8c rgedgeR/test-data/gentestdata.sh~ --- a/rgedgeR/test-data/gentestdata.sh~ Wed Jun 12 21:47:08 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,8 +0,0 @@ -#!/bin/bash -# generate test data for rgGSEA -# ross lazarus June 2013 -# adjust gseajar_path ! -GSEAJAR_PATH=/home/rlazarus/galaxy-central/tool_dependency_dir/gsea_jar/2.0.12/fubar/rg_gsea_test/8e291f464aa0/jars/gsea2-2.0.12.jar -python ../rgGSEA.py --input_tab "gsea_test_DGE.xls" --adjpvalcol "5" --signcol "2" --idcol "1" --outhtml "gseatestout.html" --input_name "gsea_test" --setMax "500" --setMin "15" --nPerm "10" --plotTop "20" --gsea_jar "$GSEAJAR_PATH" --output_dir "gseatestout" --mode "Max_probe" --title "GSEA test" --builtin_gmt "gseatestdata.gmt" - - |
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diff -r a0c04d13a7cf -r 81255a103a8c rgedgeR/tool_dependencies.xml --- a/rgedgeR/tool_dependencies.xml Wed Jun 12 21:47:08 2013 -0400 +++ b/rgedgeR/tool_dependencies.xml Wed Jun 12 23:23:05 2013 -0400 |
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@@ -1,17 +1,17 @@ <?xml version="1.0"?> <tool_dependency> <package name="r3" version="3.0.1"> - <repository changeset_revision="b90bcba24d6a" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <repository changeset_revision="addf8c9c778a" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="biocbasics" version="2.12"> <install version="1.0"> <actions> <action type="set_environment_for_install"> - <repository changeset_revision="b90bcba24d6a" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <repository changeset_revision="addf8c9c778a" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> <package name="r3" version="3.0.1" /> </repository> </action> - <action type="shell_command">$R_HOME/R CMD BATCH installBioC.R </action> + <action type="shell_command">R CMD BATCH installBioC.R </action> </actions> </install> <readme>Installs some basic bioc packages for the edgeR tool |
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diff -r a0c04d13a7cf -r 81255a103a8c rgedgeR/tool_dependencies.xml~ --- a/rgedgeR/tool_dependencies.xml~ Wed Jun 12 21:47:08 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,22 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="r3" version="3.0.1"> - <repository changeset_revision="8dcdf371a760" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> - </package> - <package name="biocbasics" version="2.12"> - <install version="1.0"> - <actions> - <action type="set_environment_for_install"> - <package name="r3" toolshed="http://testtoolshed.g2.bx.psu.edu" version="3.0.1"> - <repository name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> - </package> - - </action> - <action type="shell_command">$R_HOME/R CMD BATCH installBioC.R </action> - </actions> - </install> - <readme>Installs some basic bioc packages for the edgeR tool - - </readme> - </package> -</tool_dependency> |