Mercurial > repos > iracooke > xtandem
changeset 9:50eb60757ca5
Update
| author | Ira Cooke <iracooke@gmail.com> |
|---|---|
| date | Sun, 09 Jun 2013 08:19:31 -0500 |
| parents | 16080891c80d |
| children | ffd1d25b8080 |
| files | repository_dependencies.xml tandem.xml tool_dependencies.xml |
| diffstat | 3 files changed, 10 insertions(+), 32 deletions(-) [+] |
line wrap: on
line diff
--- a/repository_dependencies.xml Tue Mar 05 00:48:00 2013 -0500 +++ b/repository_dependencies.xml Sun Jun 09 08:19:31 2013 -0500 @@ -1,16 +1,5 @@ <?xml version="1.0"?> -<!-- <repositories description="X!Tandem requires Proteomics Datatypes as well the trans proteomic pipeline"> - <repository toolshed="http://10.211.55.28:9009" name="proteomics_datatypes" owner="iracooke" changeset_revision="699a890a9d99"/> - </repositories> - --> <repositories description="Proteomics datatypes and the TPP"> - - <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="dac478a72c1d"/> - --> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349"/> - - + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/> </repositories> -
--- a/tandem.xml Tue Mar 05 00:48:00 2013 -0500 +++ b/tandem.xml Sun Jun 09 08:19:31 2013 -0500 @@ -1,7 +1,7 @@ <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.1"> <requirements> - <requirement type="package" version="1.2.0">galaxy_protk</requirement> + <requirement type="package" version="1.2.2">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-1.2.0 do tandem_search.rb -d $database.dbkey - #else #rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.fasta_file + rvm 1.9.3@protk-1.2.2 do tandem_search.rb -d $database.dbkey + #else #rvm 1.9.3@protk-1.2.2 do tandem_search.rb -d $database.fasta_file #end if --var-mods=' @@ -121,7 +121,7 @@ <param name="variable_mods" value="15.994915@M"/> <param name="fixed_mods" value="57.021464@C"/> <param name="allow_multi_isotope_search" value="false"/> - <output name="output" file="bsa.pepXML" compare="sim_size" delta="100" /> + <output name="output" file="bsa.pepXML" compare="sim_size" delta="600" /> </test> </tests>
--- a/tool_dependencies.xml Tue Mar 05 00:48:00 2013 -0500 +++ b/tool_dependencies.xml Sun Jun 09 08:19:31 2013 -0500 @@ -1,21 +1,10 @@ <?xml version="1.0"?> <tool_dependency> -<!-- <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 name="galaxy_protk" version="1.2.2"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/> </package> <package name="trans_proteomic_pipeline" version="4.6.1"> - <repository toolshed="http://10.211.55.28:9009" name="protk_tpp" owner="iracooke" changeset_revision="e44f0d3bb9dd" /> - </package> - --> - <package name="galaxy_protk" version="1.2.0"> - <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="e85a18371516"/> </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="cedd5e884349" /> - </package> - - - -</tool_dependency> \ No newline at end of file +</tool_dependency>