| Previous changeset 4:4facf54f380c (2013-03-04) Next changeset 6:a5414905da0f (2013-03-05) |
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Commit message:
Uploaded |
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modified:
repository_dependencies.xml tandem.xml tool_dependencies.xml |
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added:
README |
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| diff -r 4facf54f380c -r 0c2ee2a55613 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Mar 05 00:29:58 2013 -0500 |
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| @@ -0,0 +1,5 @@ +This package installs a wrapper script for the X!Tandem search engine + +Requirements: +This package depends on the galaxy_protk and protk_trans_proteomic_pipeline packages +Please see instructions for those packages before installing |
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| diff -r 4facf54f380c -r 0c2ee2a55613 repository_dependencies.xml --- a/repository_dependencies.xml Mon Mar 04 18:41:50 2013 -0500 +++ b/repository_dependencies.xml Tue Mar 05 00:29:58 2013 -0500 |
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| @@ -5,11 +5,11 @@ --> <repositories description="Proteomics datatypes and the TPP"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="463328a6967f"/> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="f302406a0297"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349"/> </repositories> |
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| diff -r 4facf54f380c -r 0c2ee2a55613 tandem.xml --- a/tandem.xml Mon Mar 04 18:41:50 2013 -0500 +++ b/tandem.xml Tue Mar 05 00:29:58 2013 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.0"> +<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.1"> <requirements> - <requirement type="package" version="1.1.9">galaxy_protk</requirement> + <requirement type="package" version="1.2.0">galaxy_protk</requirement> <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> </requirements> @@ -9,8 +9,8 @@ <command> #if $database.source_select=="built_in": - rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.dbkey - #else #rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.fasta_file + rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.dbkey + #else #rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.fasta_file #end if --var-mods=' |
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| diff -r 4facf54f380c -r 0c2ee2a55613 tool_dependencies.xml --- a/tool_dependencies.xml Mon Mar 04 18:41:50 2013 -0500 +++ b/tool_dependencies.xml Tue Mar 05 00:29:58 2013 -0500 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> -<!-- <package name="galaxy_protk" version="1.1.9"> +<!-- <package name="galaxy_protk" version="1.2.0"> <repository toolshed="http://10.211.55.28:9009" name="galaxy_protk" owner="iracooke" changeset_revision="5610168f3b53"/> </package> @@ -8,12 +8,12 @@ <repository toolshed="http://10.211.55.28:9009" name="protk_tpp" owner="iracooke" changeset_revision="e44f0d3bb9dd" /> </package> --> - <package name="galaxy_protk" version="1.1.9"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/> + <package name="galaxy_protk" version="1.2.0"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/> </package> <package name="trans_proteomic_pipeline" version="4.6.1"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="f302406a0297" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349" /> </package> |