Mercurial > repos > galaxyp > peptide_to_gff
changeset 1:0cd177bc347d
Update tool dependencies
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 08 Sep 2014 13:36:17 -0500 |
| parents | cec60c540546 |
| children | 4c87b4cc1176 |
| files | peptide_to_gff.xml repository_dependencies.xml requirements.txt tool_dependencies.xml |
| diffstat | 4 files changed, 15 insertions(+), 16 deletions(-) [+] |
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--- a/peptide_to_gff.xml Wed Jun 26 15:56:16 2013 -0400 +++ b/peptide_to_gff.xml Mon Sep 08 13:36:17 2014 -0500 @@ -1,8 +1,10 @@ <tool id="peptide_to_gff" name="Peptide to GFF" version="1.0"> <description>Map peptide to reference genome</description> <requirements> - <requirement type="package">kent_tools</requirement> - <requirement type="package" version="master">peptide_to_gff</requirement> + <requirement type="package" version="35x1">blat</requirement> + <requirement type="package" version="1.61">biopython</requirement> + <requirement type="package" version="0.1">bcbb_gff</requirement> + <requirement type="package" version="0.1">peptide_to_gff</requirement> </requirements> <command>peptide_to_gff #if $peptide_src.inputFormat == 'protein_pilot' or $peptide_src.inputFormat == 'tabular':
--- a/repository_dependencies.xml Wed Jun 26 15:56:16 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -hg clone ssh://hg@bitbucket.org/galaxyp/galaxyp-toolshed-peptides-to-gff
--- a/requirements.txt Wed Jun 26 15:56:16 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -numpy -biopython==1.61 -bcbio-gff
--- a/tool_dependencies.xml Wed Jun 26 15:56:16 2013 -0400 +++ b/tool_dependencies.xml Mon Sep 08 13:36:17 2014 -0500 @@ -1,14 +1,15 @@ <?xml version="1.0"?> <tool_dependency> - <package name="peptide_to_gff" version="master"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://bitbucket.org/galaxyp/peptide_to_gff/get/5f32b86.tar.gz</action> - <action type="setup_virtualenv" /> - </actions> - </install> - <readme> - Sets up a virtualenv for peptides-to-gff. - </readme> + <package name="biopython" version="1.61"> + <repository name="package_biopython_1_61" owner="biopython" changeset_revision="ae9dda584395" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bcbb_gff" version="0.1"> + <repository name="bcbb_gff_0_1" owner="galaxyp" changeset_revision="886eb2f99232" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="peptide_to_gff" version="0.1"> + <repository name="package_peptides_to_gff_0_1" owner="galaxyp" changeset_revision="986d1d024720" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="blat" version="35x1"> + <repository name="package_blat_35x1" owner="iuc" changeset_revision="cc0f4b49b6f1" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>