Mercurial > repos > fubar > htseq_bams_to_count_matrix
changeset 13:76297e1ef552 draft
almost right - testing adding requirements
| author | fubar |
|---|---|
| date | Thu, 06 Jun 2013 22:14:16 -0400 |
| parents | 71f4b3d0e681 |
| children | b227f5edbe52 |
| files | htseq_bams_to_count_matrix/htseqsams2mx.xml htseq_bams_to_count_matrix/tool_dependencies.xml |
| diffstat | 2 files changed, 5 insertions(+), 6 deletions(-) [+] |
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--- a/htseq_bams_to_count_matrix/htseqsams2mx.xml Thu Jun 06 21:48:09 2013 -0400 +++ b/htseq_bams_to_count_matrix/htseqsams2mx.xml Thu Jun 06 22:14:16 2013 -0400 @@ -1,10 +1,10 @@ <tool id="htseqsams2mx" name="Multiple SAMs to count matrix" version="0.2"> <description>for DGE</description> <requirements> - <requirement type="package" version="0.5.4p3">package_htseq_0_5_4</requirement> - <!-- <requirement type="package" version="2.4.11">freetype</requirement> - <requirement type="package" version="1.7.1">package_numpy_1_7</requirement> - <requirement type="package" version="1.2.1">matplotlib</requirement> --> + <requirement type="package" version="0.5.4p3">htseq</requirement> + <requirement type="package" version="2.4.11">freetype</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="1.2.1">matplotlib</requirement> </requirements> <command interpreter="python"> htseqsams2mx.py -g "$gfffile" -o "$outfile" -m "$model" --id_attribute "$id_attr" --feature_type "$feature_type"
--- a/htseq_bams_to_count_matrix/tool_dependencies.xml Thu Jun 06 21:48:09 2013 -0400 +++ b/htseq_bams_to_count_matrix/tool_dependencies.xml Thu Jun 06 22:14:16 2013 -0400 @@ -11,7 +11,6 @@ <actions> <!-- first action is always downloading --> <action type="download_by_url">http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.2.1/matplotlib-1.2.1.tar.gz</action> - <!-- populate the environment variables from the dependend repos --> <action type="set_environment_for_install"> <package name="numpy" toolshed="http://testtoolshed.g2.bx.psu.edu" version="1.7.1"> @@ -37,7 +36,7 @@ </install> <readme>Compiling matplotlib requires a C compiler (typically gcc) and libpng.</readme> </package> - <package name="package_htseq_0_5_4" version="0.5.4p3"> + <package name="htseq" version="0.5.4p3"> <install version="1.0"> <actions> <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action>