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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_tophat2_2_0_9 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 18:47:37 -0500
parents bac5f59d20d8
children
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<?xml version="1.0"?>
<tool_dependency>
  <package name="tophat2" version="2.0.9">
      <install version="1.0">
          <actions_group>
              <actions architecture="x86_64" os="linux">
                  <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/tophat/tophat-2.0.9.Linux_x86_64.tar.gz</action>
                    <action type="move_directory_files">
                      <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>
                <actions architecture="x86_64" os="darwin">
                  <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/tophat/tophat-2.0.9.OSX_x86_64.tar.gz</action>
                    <action type="move_directory_files">
                      <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>
                <actions>
                  <package name="samtools" version="0.1.18">
                      <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <action type="download_by_url">http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.9.tar.gz</action>
                    <action type="set_environment_for_install">
                      <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                    </action>
                    <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-bam=$BAM_ROOT</action>
                    <action type="shell_command">make &amp;&amp; make install</action>
                </actions>
                <action type="set_environment">
                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme />
    </package>
</tool_dependency>