| Previous changeset 0:1049de3f4aed (2013-01-06) Next changeset 2:37a41ca93b5e (2013-03-04) |
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Commit message:
Uploaded |
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modified:
msgfplus_search.xml |
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added:
README repository_dependencies.xml tool_dependencies.xml |
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| diff -r 1049de3f4aed -r 50002ff2c1f3 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Mar 04 20:17:25 2013 -0500 |
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| @@ -0,0 +1,6 @@ +This package is an installer for the MSGF+ search tool. + +System Requirements. Ensure that you have the following packages installed on your system +- unzip +- java runtime 6 or higher + |
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| diff -r 1049de3f4aed -r 50002ff2c1f3 msgfplus_search.xml --- a/msgfplus_search.xml Sun Jan 06 20:06:08 2013 -0500 +++ b/msgfplus_search.xml Mon Mar 04 20:17:25 2013 -0500 |
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| @@ -1,11 +1,28 @@ <tool id="proteomics_search_msgfplus_1" name="MSGF+ 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="20121116">protk_msgfplus</requirement> + </requirements> + + <description>Run an MSGF+ Search</description> + + + <description>Run an X!Tandem Search</description> + <command> #if $database.source_select=="built_in": - msgfplus_search.rb --galaxy -d $database.dbkey --java-mem 8000M - #else #msgfplus_search.rb -d $database.fasta_file + 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 + #end if + + + <command> + #if $database.source_select=="built_in": + rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb --galaxy -d $database.dbkey + #else #rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb -d $database.fasta_file #end if --var-mods=' |
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| diff -r 1049de3f4aed -r 50002ff2c1f3 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Mar 04 20:17:25 2013 -0500 |
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| @@ -0,0 +1,10 @@ +<?xml version="1.0"?> +<repositories description="Proteomics datatypes, MSGF+ and Protk"> + + <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="protk_msgfplus" owner="iracooke" changeset_revision="528bcbb94199"/> + + </repositories> |
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| diff -r 1049de3f4aed -r 50002ff2c1f3 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Mar 04 20:17:25 2013 -0500 |
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| @@ -0,0 +1,13 @@ +<?xml version="1.0"?> +<tool_dependency> + + <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="msgfplus" version="20130227"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="528bcbb94199"/> + </package> + + +</tool_dependency> \ No newline at end of file |