comparison tool_dependencies.xml @ 1:ccadfae70b02 draft

Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation.

0:58e1eb37fddc

<tool_dependency>
  <package name="bwa" version="0.6.2">
    <repository changeset_revision="0778635a84ba" name="package_bwa_0_6_2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="blat" version="35">
<!--    <repository name="package_blat_35x1" owner="iuc" /> This may be used instead of everything inside <install> when a stable Galaxy release will support the 'download_binary' action type -->
  </package>
  <package name="sequel" version="1.0.2">
    <install version="1.0">
      <actions>
        <action target_filename="SEQuel.tar.gz" type="download_by_url">http://bix.ucsd.edu/SEQuel/download/SEQuel.v102.tar.gz</action>

          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
        </action>
        <action type="set_environment">
          <environment_variable action="set_to" name="SEQUEL_JAR_PATH">$INSTALL_DIR</environment_variable>
        </action>
        <action type="set_environment">
          <environment_variable action="set_to" name="SEQUEL_SITE_OPTIONS">"-t 8 -p 8 -u 1"</environment_variable>
        </action>
      </actions>
    </install>
    <readme>
Change the SEQUEL_SITE_OPTIONS variable in the installed env.sh file to adjust the number of threads to use in BWA alignment (-t) or the maximum number of threads for SEQuel (-p) or the minimum number of threads for SEQuel (-u).
    </readme>
  </package>
</tool_dependency>

1:ccadfae70b02

<tool_dependency>
  <package name="bwa" version="0.6.2">
    <repository changeset_revision="0778635a84ba" name="package_bwa_0_6_2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="blat" version="35">
    <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="sequel" version="1.0.2">
    <install version="1.0">
      <actions>
        <action target_filename="SEQuel.tar.gz" type="download_by_url">http://bix.ucsd.edu/SEQuel/download/SEQuel.v102.tar.gz</action>

          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
        </action>
        <action type="set_environment">
          <environment_variable action="set_to" name="SEQUEL_JAR_PATH">$INSTALL_DIR</environment_variable>
        </action>
      </actions>
    </install>
    <readme>
Configuration: Previously (until Release 0), the SEQUEL_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use in BWA alignment (-t) or the maximum number of threads for SEQuel (-p) or the minimum number of threads for SEQuel (-u). This is not used anymore and may be removed.
    </readme>
  </package>
</tool_dependency>