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README msgfplus_search.xml repository_dependencies.xml tool_dependencies.xml |
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| diff -r ce2f26664c9d -r b3f2bd49029c README --- a/README Mon Mar 04 21:44:52 2013 -0500 +++ b/README Tue Mar 05 00:20:42 2013 -0500 |
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| @@ -1,16 +1,7 @@ This package is a galaxy wrapper for the MSGF+ search tool. -The underlying MSGF+ tool itself should be automatically installed however you must -satisfy the requirements below before attempting to install. - -System Requirements. Ensure that you have the following packages installed on your system +Requirements: +This package depends on the galaxy_protk and protk_msgfplus and protk_proteowizard packages +Please see instructions for those packages before installing -(For protk_msgfplus) -- unzip -- java runtime 6 or higher - -(For galaxy_protk) -- The ability to download files (an internet connection): curl wget -- gcc g++ make autoconf automake libtool pkg-config patch git openssl -libreadline6 libreadline6-dev git-core zlib1g zlib1g-dev libssl-dev -libc6-dev ncurses-dev bison subversion libxml2 libxml2-dev +In addition to basic requirements you must also have unzip and java 6 runtime (or greater) installed |
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| diff -r ce2f26664c9d -r b3f2bd49029c msgfplus_search.xml --- a/msgfplus_search.xml Mon Mar 04 21:44:52 2013 -0500 +++ b/msgfplus_search.xml Tue Mar 05 00:20:42 2013 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.0"> +<tool id="proteomics_search_msgfplus_1" name="MSGF+ 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="20130227">msgfplus</requirement> <requirement type="package" version="3_0_4388">proteowizard</requirement> </requirements> @@ -11,8 +11,8 @@ <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 + rvm 1.9.3@protk-1.2.0 do msgfplus_search.rb --galaxy -d $database.dbkey + #else #rvm 1.9.3@protk-1.2.0 do msgfplus_search.rb --galaxy -d $database.fasta_file #end if --var-mods=' |
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| diff -r ce2f26664c9d -r b3f2bd49029c repository_dependencies.xml --- a/repository_dependencies.xml Mon Mar 04 21:44:52 2013 -0500 +++ b/repository_dependencies.xml Tue Mar 05 00:20:42 2013 -0500 |
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| @@ -3,10 +3,10 @@ <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_msgfplus" owner="iracooke" changeset_revision="87757d28e0d2"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="21c7f6a61d61"/> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="6ead3520e93a"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="dd22a794a86b"/> </repositories> |
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| diff -r ce2f26664c9d -r b3f2bd49029c tool_dependencies.xml --- a/tool_dependencies.xml Mon Mar 04 21:44:52 2013 -0500 +++ b/tool_dependencies.xml Tue Mar 05 00:20:42 2013 -0500 |
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| @@ -1,16 +1,16 @@ <?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 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="proteowizard" version="3_0_4388"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="6ead3520e93a"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="dd22a794a86b"/> </package> <package name="msgfplus" version="20130227"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="87757d28e0d2"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="21c7f6a61d61"/> </package> |