| Previous changeset 0:5e1594a15956 (2013-01-06) Next changeset 2:5ba3d95534a5 (2013-03-04) |
|
Commit message:
Uploaded |
|
modified:
omssa.xml |
|
added:
.DS_Store ._.DS_Store repository_dependencies.xml tool_dependencies.xml |
| b |
| diff -r 5e1594a15956 -r 21cede3cfb9b .DS_Store |
| b |
| Binary file .DS_Store has changed |
| b |
| diff -r 5e1594a15956 -r 21cede3cfb9b ._.DS_Store |
| b |
| Binary file ._.DS_Store has changed |
| b |
| diff -r 5e1594a15956 -r 21cede3cfb9b omssa.xml --- a/omssa.xml Sun Jan 06 20:03:20 2013 -0500 +++ b/omssa.xml Mon Mar 04 04:22:23 2013 -0500 |
| b |
| @@ -1,13 +1,17 @@ <tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.0"> - <requirements> - <requirement type="package">protkgem</requirement> - </requirements> - + + <requirements> + <requirement type="package" version="1.1.9">galaxy_protk</requirement> + <requirement type="package" version="2.1.8">omssa</requirement> + <requirement type="package" version="2.2.27">blast</requirement> + </requirements> + + <description>Run an OMSSA MS/MS Search</description> <command>#if $database.source_select=="built_in": - omssa_search.rb -d $database.dbkey - #else #omssa_search.rb -d $database.fasta_file + 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 #end if --var-mods=' |
| b |
| diff -r 5e1594a15956 -r 21cede3cfb9b repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Mar 04 04:22:23 2013 -0500 |
| b |
| @@ -0,0 +1,10 @@ +<?xml version="1.0"?> +<!-- <repositories description="Requires Proteomics Datatypes"> + <repository toolshed="http://10.211.55.28:9009" name="proteomics_datatypes" owner="iracooke" changeset_revision="699a890a9d99"/> + </repositories> + --> + + + <repositories description="Requires the protk rubygem to install omssa"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/> +</repositories> \ No newline at end of file |
| b |
| diff -r 5e1594a15956 -r 21cede3cfb9b tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Mar 04 04:22:23 2013 -0500 |
| b |
| @@ -0,0 +1,29 @@ +<?xml version="1.0"?> +<tool_dependency> + <!-- <package name="galaxy_protk" version="1.1.9"> + <repository toolshed="http://10.211.55.28:9009" name="galaxy_protk" owner="iracooke" changeset_revision="5610168f3b53"/> + </package> + + <package name="blast" version="2.2.27"> + <repository toolshed="http://10.211.55.28:9009" name="protk_blast" owner="iracooke" changeset_revision="0f3b7bbdfdd4" /> + </package> + + <package name="omssa" version="2.1.8"> + <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> + + <package name="blast" version="2.2.27"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="88ada6a29993" /> + </package> + + <package name="omssa" version="2.1.8"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="e924c0d646d0" /> + </package> + + + +</tool_dependency> \ No newline at end of file |