annotate tool_dependencies.xml @ 2:208ce57f9221 draft default tip

Fix version for blat requirement (reported by Bjoern Gruening). Upgrade BWA dependency to v. 0.7.7 . Update Orione citation.

<?xml version="1.0"?>
<tool_dependency>
  <package name="bwa" version="0.7.7">
    <repository changeset_revision="def70e393020" name="package_bwa_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="blat" version="35x1">
    <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>
        <action type="move_directory_files">
          <source_directory>.</source_directory>
          <destination_directory>$INSTALL_DIR</destination_directory>
        </action>
        <action type="set_environment">
          <environment_variable action="prepend_to" name="PATH">$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>