view tool_dependencies.xml @ 2:00d73c812399 draft

Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2.

<?xml version="1.0"?>
<tool_dependency>
  <!-- Dependencies from main/test toolsheds -->
  <package name="numpy" version="1.9">
    <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="R" version="3.1.2">
    <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <!-- Subset of UCSC tools -->
  <package name="ucsc_tools_for_macs21" version="2.0">
      <install version="1.0">
            <actions>
	      <!-- fetchChromSizes -->
              <action type="download_binary">
                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
              </action>
              <action type="chmod">
                <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
              </action>
	      <!-- bedClip -->
              <action type="download_binary">
                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template>
              </action>
              <action type="chmod">
                <file mode="755">$INSTALL_DIR/bedClip</file>
              </action>
	      <!-- bedSort -->
              <action type="download_binary">
                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedSort</url_template>
              </action>
              <action type="chmod">
                <file mode="755">$INSTALL_DIR/bedSort</file>
              </action>
	      <!-- bedGraphToBigWig -->
              <action type="download_binary">
                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
              </action>
              <action type="chmod">
                <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
              </action>
              <action type="set_environment">
                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
              </action>
	    </actions>
      </install>
  </package>
  <!-- MACS 2.1.0 -->
  <package name="macs2" version="2.1.0.20140616">
      <install version="1.0">
            <actions>
              <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action>
	      <!-- Install environment for main & test toolsheds -->
              <action type="set_environment_for_install">
		<repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
		  <package name="numpy" version="1.9" />
		</repository>
	      </action>
              <action type="make_directory">$INSTALL_DIR/lib/python</action>
              <action type="shell_command">
                export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
              </action>
              <action type="set_environment">
                <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
              </action>
            </actions>
      </install>
      <readme>Macs2.1 depends on having python2.7 and numpy 1.8 installed on all nodes of the work cluster</readme>
    </package>
</tool_dependency>