Mercurial > repos > biomonika > test_dependency
changeset 15:9c08f9866ce6
d7
| author | biomonika <biomonika@psu.edu> |
|---|---|
| date | Mon, 25 Aug 2014 15:09:49 -0400 |
| parents | 7558fc0db1cf |
| children | 76917da4e1ac |
| files | test_dependency.xml tool_dependencies.xml |
| diffstat | 2 files changed, 3 insertions(+), 1 deletions(-) [+] |
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--- a/test_dependency.xml Mon Aug 25 14:55:16 2014 -0400 +++ b/test_dependency.xml Mon Aug 25 15:09:49 2014 -0400 @@ -6,8 +6,9 @@ <requirement type="package" version="0.1.19">samtools</requirement> </requirements> </requirements> - <command interpreter="bash">test_dependency.sh $output</command> + <command interpreter="bash">test_dependency.sh $output $input1</command> <inputs> + <param format="fastq" name="input1" type="data" label="Reference"/> </inputs> <outputs> <data format="txt" name="output" />
--- a/tool_dependencies.xml Mon Aug 25 14:55:16 2014 -0400 +++ b/tool_dependencies.xml Mon Aug 25 15:09:49 2014 -0400 @@ -7,6 +7,7 @@ <install version="1.0"> <actions> <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> + <action type="shell_command">sed -i .bak -e 's/O2/O2 -fPIC/‘ Makefile</action> <action type="shell_command">make</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>