Mercurial > repos > bgruening > diffbind
changeset 11:a8dc71379df0 draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 17 Jan 2014 04:04:16 -0500 |
| parents | b1b96b6ed60c |
| children | 43884541e66f |
| files | diffbind.R diffbind.xml tool_dependencies.xml |
| diffstat | 3 files changed, 6 insertions(+), 5 deletions(-) [+] |
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--- a/diffbind.R Thu Jan 16 04:17:16 2014 -0500 +++ b/diffbind.R Fri Jan 17 04:04:16 2014 -0500 @@ -27,9 +27,7 @@ q(status=1); } - library('DiffBind') -# used to save to BED, GFF or WIG format if ( !is.null(opt$plots) ) { pdf(opt$plots)
--- a/diffbind.xml Thu Jan 16 04:17:16 2014 -0500 +++ b/diffbind.xml Fri Jan 17 04:04:16 2014 -0500 @@ -6,6 +6,7 @@ <requirement type="package" version="3.0.1">R_3_0_1</requirement> <requirement type="package" version="1.0.17">deseq2</requirement> <requirement type="package" version="1.8.3">diffbind</requirement> + <requirement type="set_environment">DIFFBIND_SCRIPT_PATH</requirement> </requirements> <command> ## seems that diffbind also needs file extensions to work properly @@ -18,7 +19,7 @@ #set $counter = $counter + 1 #end for - Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/diffbind/7929c8b3f6f9/diffbind/diffbind.R + Rscript \$AUGUSTUS_SCRIPT_PATH/diffbind.R -i $infile -o $outfile -p $plots
--- a/tool_dependencies.xml Thu Jan 16 04:17:16 2014 -0500 +++ b/tool_dependencies.xml Fri Jan 17 04:04:16 2014 -0500 @@ -4,9 +4,11 @@ <repository changeset_revision="0a395bcd7efd" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="deseq2" version="1.0.17"> - <repository changeset_revision="3b6a8c377895" name="package_deseq2_1_0_17" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c62e0a0f4fed" name="package_deseq2_1_0_17" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - + <set_environment version="1.0"> + <environment_variable action="set_to" name="DIFFBIND_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> <package name="diffbind" version="1.8.3"> <install version="1.0"> <actions>