Mercurial > repos > pjbriggs > ceas
changeset 2:695d61decd06 draft
Make dependency on R explicit.
| author | pjbriggs |
|---|---|
| date | Tue, 21 Apr 2015 10:56:47 -0400 |
| parents | d9032bb158b9 |
| children | 82df5af2995f |
| files | ceasbw_wrapper.sh ceasbw_wrapper.xml tool_dependencies.xml |
| diffstat | 3 files changed, 18 insertions(+), 5 deletions(-) [+] |
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--- a/ceasbw_wrapper.sh Wed Jan 28 05:04:46 2015 -0500 +++ b/ceasbw_wrapper.sh Tue Apr 21 10:56:47 2015 -0400 @@ -20,6 +20,13 @@ if [ "$7" == "--bigwig" ] ; then CEAS=ceasBW fi + if [ "$7" == "--length" ] ; then + chrom_sizes=$8 + if [ ! -f "$chrom_sizes" ] ; then + echo "ERROR no file $chrom_sizes, stopping" >&2 + exit 1 + fi + fi OPTIONS="$OPTIONS $7" shift done
--- a/ceasbw_wrapper.xml Wed Jan 28 05:04:46 2015 -0500 +++ b/ceasbw_wrapper.xml Tue Apr 21 10:56:47 2015 -0400 @@ -1,4 +1,10 @@ <tool id="ceasbw" name="CEAS" version="1.0.2-0"> + <requirements> + <requirement type="package" version="1.2.5">python_mysqldb</requirement> + <requirement type="package" version="0.7.1">bx_python</requirement> + <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement> + <requirement type="package" version="3.1.2">R</requirement> + </requirements> <description>Annotate intervals and scores with genome features (cistrome CEAS)</description> <command interpreter="bash">ceasbw_wrapper.sh $bed_file $gdb_file $extra_bed_file $log_output $pdf_report $xls_output #if (str($wig_file.ext) == 'bigwig') @@ -14,11 +20,6 @@ --bisizes $bisizes_lower,$bisizes_upper --pf-res $profiling_resolution --rel-dist $relative_distance</command> - <requirements> - <requirement type="package" version="1.2.5">python_mysqldb</requirement> - <requirement type="package" version="0.7.1">bx_python</requirement> - <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement> - </requirements> <inputs> <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" /> <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true" />
--- a/tool_dependencies.xml Wed Jan 28 05:04:46 2015 -0500 +++ b/tool_dependencies.xml Tue Apr 21 10:56:47 2015 -0400 @@ -1,5 +1,10 @@ <?xml version="1.0"?> <tool_dependency> + <!-- Dependencies from main/test toolsheds --> + <package name="R" version="3.1.2"> + <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <!-- Python mysqldb package --> <package name="python_mysqldb" version="1.2.5"> <install version="1.0"> <actions>