| Previous changeset 1:cd0d5e6b9a92 (2013-06-06) Next changeset 3:ae9195035aa6 (2013-09-26) |
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Commit message:
Use setup_rvm action |
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modified:
omssa.xml repository_dependencies.xml tool_dependencies.xml |
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| diff -r cd0d5e6b9a92 -r e79b95501048 omssa.xml --- a/omssa.xml Thu Jun 06 15:37:22 2013 +1000 +++ b/omssa.xml Thu Sep 26 14:09:13 2013 +1000 |
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| @@ -9,7 +9,7 @@ <description>Run an OMSSA MS/MS Search</description> - <command>rvm 1.9.3@protk-1.2.2 do omssa_search.rb + <command>omssa_search.rb #if $database.source_select=="built_in": -d $database.dbkey |
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| diff -r cd0d5e6b9a92 -r e79b95501048 repository_dependencies.xml --- a/repository_dependencies.xml Thu Jun 06 15:37:22 2013 +1000 +++ b/repository_dependencies.xml Thu Sep 26 14:09:13 2013 +1000 |
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| @@ -3,10 +3,10 @@ <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="7101f7e4b00b"/> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="32c643142290" prior_installation_required="True"/> +<!-- <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d" prior_installation_required="True"/> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="a1b21b3844c8"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="0d86d29aaed6" /> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="b386c6c95d0e"/> - + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="f77532db59b6" /> + --> </repositories> |
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| diff -r cd0d5e6b9a92 -r e79b95501048 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jun 06 15:37:22 2013 +1000 +++ b/tool_dependencies.xml Thu Sep 26 14:09:13 2013 +1000 |
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| @@ -1,18 +1,18 @@ <?xml version="1.0"?> <tool_dependency> - - <package name="galaxy_protk" version="1.2.2"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="32c643142290" prior_installation_required="True"/> - </package> - - <package name="blast" version="2.2.27"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="a1b21b3844c8"/> - </package> - - <package name="omssa" version="2.1.9"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="b386c6c95d0e"/> - </package> - - + <package name="protk_omssa" version="2.1.9"> + <install version="1.0"> + <actions> + <action type="setup_rvm" ruby="1.9.3-p448"> + <gem version="1.2.4">protk</gem> + </action> + <action type="shell_command">protk_setup.rb blast</action> + <action type="shell_command">protk_setup.rb omssa</action> + </actions> + </install> + <readme> + RVM Example + </readme> + </package> </tool_dependency> |