| Previous changeset 2:5ba3d95534a5 (2013-03-04) Next changeset 4:54b870eaca8d (2013-06-09) |
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Commit message:
Uploaded |
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modified:
omssa.xml repository_dependencies.xml tool_dependencies.xml |
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added:
README |
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| diff -r 5ba3d95534a5 -r 155b6449fdf3 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Mar 05 00:25:34 2013 -0500 |
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| @@ -0,0 +1,5 @@ +This package installs wrapper scripts for running OMSSA MS/MS searches + +Requirements: +This package depends on the galaxy_protk, protk_omssa and protk_blast packages +Please see instructions for those packages before installing |
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| diff -r 5ba3d95534a5 -r 155b6449fdf3 omssa.xml --- a/omssa.xml Mon Mar 04 18:40:07 2013 -0500 +++ b/omssa.xml Tue Mar 05 00:25:34 2013 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.0"> +<tool id="proteomics_search_omssa_1" name="OMSSA 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="2.1.8">omssa</requirement> <requirement type="package" version="2.2.27">blast</requirement> </requirements> @@ -10,8 +10,8 @@ <description>Run an OMSSA MS/MS Search</description> <command>#if $database.source_select=="built_in": - rvm 1.9.3@protk-1.1.9 do omssa_search.rb -d $database.dbkey - #else #rvm 1.9.3@protk-1.1.9 do omssa_search.rb -d $database.fasta_file + rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.dbkey + #else #rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.fasta_file #end if --var-mods=' |
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| diff -r 5ba3d95534a5 -r 155b6449fdf3 repository_dependencies.xml --- a/repository_dependencies.xml Mon Mar 04 18:40:07 2013 -0500 +++ b/repository_dependencies.xml Tue Mar 05 00:25:34 2013 -0500 |
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| @@ -6,13 +6,13 @@ <repositories description="Proteomics datatypes, omssa and blast executables"> - <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="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="protk_blast" owner="iracooke" changeset_revision="88ada6a29993" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="0d86d29aaed6" /> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="e924c0d646d0" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="f77532db59b6" /> </repositories> \ No newline at end of file |
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| diff -r 5ba3d95534a5 -r 155b6449fdf3 tool_dependencies.xml --- a/tool_dependencies.xml Mon Mar 04 18:40:07 2013 -0500 +++ b/tool_dependencies.xml Tue Mar 05 00:25:34 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> @@ -12,16 +12,16 @@ <repository toolshed="http://10.211.55.28:9009" name="protk_omssa" owner="iracooke" changeset_revision="117faa58df2a" /> </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="blast" version="2.2.27"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="88ada6a29993" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="0d86d29aaed6" /> </package> <package name="omssa" version="2.1.8"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="e924c0d646d0" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="f77532db59b6" /> </package> |