| Previous changeset 25:552607114655 (2013-06-12) Next changeset 27:2c5d462ee8e9 (2013-06-12) |
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Commit message:
Uploaded |
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modified:
rgedgeR/tool_dependencies.xml |
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added:
rgedgeR/test-data/gentestdata.sh~ rgedgeR/tool_dependencies.xml~ |
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| diff -r 552607114655 -r db24a3130845 rgedgeR/test-data/gentestdata.sh~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgedgeR/test-data/gentestdata.sh~ Wed Jun 12 19:58:03 2013 -0400 |
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| @@ -0,0 +1,8 @@ +#!/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 "$GSEAJAR_PATH" --output_dir "gseatestout" --mode "Max_probe" --title "GSEA test" --builtin_gmt "gseatestdata.gmt" + + |
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| diff -r 552607114655 -r db24a3130845 rgedgeR/tool_dependencies.xml --- a/rgedgeR/tool_dependencies.xml Wed Jun 12 19:27:29 2013 -0400 +++ b/rgedgeR/tool_dependencies.xml Wed Jun 12 19:58:03 2013 -0400 |
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| @@ -1,16 +1,15 @@ <?xml version="1.0"?> <tool_dependency> <package name="r3" version="3.0.1"> - <repository changeset_revision="8dcdf371a760" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <repository changeset_revision="8f91c9b85935" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="biocbasics" version="2.12"> <install version="1.0"> <actions> <action type="set_environment_for_install"> - <package name="r3" toolshed="http://testtoolshed.g2.bx.psu.edu" version="3.0.1"> - <repository name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> - </package> - + <package name="r3" toolshed="http://testtoolshed.g2.bx.psu.edu" version="3.0.1"> + <repository name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> </action> <action type="shell_command">$R_HOME/R CMD BATCH installBioC.R </action> </actions> |
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| diff -r 552607114655 -r db24a3130845 rgedgeR/tool_dependencies.xml~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgedgeR/tool_dependencies.xml~ Wed Jun 12 19:58:03 2013 -0400 |
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| @@ -0,0 +1,22 @@ +<?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> |