Mercurial > repos > bgruening > deseq2
changeset 18:72613128bd65 draft
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 30 Sep 2013 11:15:24 -0400 |
| parents | a05999fd6e26 |
| children | a1aa11e02862 |
| files | deseq2.xml tool_dependencies.xml |
| diffstat | 2 files changed, 6 insertions(+), 5 deletions(-) [+] |
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--- a/deseq2.xml Mon Sep 30 10:51:41 2013 -0400 +++ b/deseq2.xml Mon Sep 30 11:15:24 2013 -0400 @@ -4,7 +4,8 @@ <requirement type="binary">Rscript</requirement> <requirement type="R-module">DESeq2</requirement> <requirement type="package" version="3.0.1">R_3_0_1</requirement> - <requirement type="set_environment">DESEQ2_SCRIPT_PATH</requirement> + <requirement type="package" version="1.0.17">deseq2</requirement> + <!--<requirement type="set_environment">DESEQ2_SCRIPT_PATH</requirement>--> </requirements> <command interpreter="Rscript"> #import simplejson @@ -20,7 +21,7 @@ #set $temp_factor_name = list() #for $factor in $rep_factorName: - #set $temp_factor = dict() + #set $temp_factor = dict() #for $level in $factor.rep_factorLevel: ##$temp_factor_list.append( '%s::%s:%s' % ($factor.factorName.replace(' ','_'), $level.factorLevel, $level.factorIndex) ) $temp_factor.update({str($level.factorLevel): map(int, str($level.factorIndex).split(','))})
--- a/tool_dependencies.xml Mon Sep 30 10:51:41 2013 -0400 +++ b/tool_dependencies.xml Mon Sep 30 11:15:24 2013 -0400 @@ -6,7 +6,7 @@ <package name="deseq2" version="1.0.17"> <repository changeset_revision="3e3d1a50a347" name="package_deseq2_1_0_17" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - <set_environment version="1.0"> - <environment_variable action="set_to" name="DESEQ2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR/scripts</environment_variable> - </set_environment> + <!--<set_environment version="1.0"> + <environment_variable name="DESEQ2_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR/scripts</environment_variable> + </set_environment>--> </tool_dependency>