view tool_dependencies.xml @ 1:df9033b88b53 draft

Fix data manager for Galaxy version v16.04 (was failing with import error for 'six' package)

<?xml version="1.0"?>
<tool_dependency>
  <!-- Local version of R 3.1.2 dependency -->
  <package name="R" version="3.1.2">
    <install version="1.0">
      <actions>
	<action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.2.tar.gz</action>
        <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
        <action type="make_install" />
        <action type="set_environment">
          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
        </action>
      </actions>
    </install>
  </package>
  <!-- Python mysqldb package -->
  <package name="python_mysqldb" version="1.2.5">
    <install version="1.0">
      <actions>
	<action type="download_by_url">https://pypi.python.org/packages/source/M/MySQL-python/MySQL-python-1.2.5.zip</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">$INSTALL_DIR/bin</environment_variable>
        </action>
      </actions>
    </install>
    <readme>Installs Python module MySQLdb 1.2.5</readme>
  </package>
  <!-- bx_python
       This is cribbed from devteam's 'package_bx_python_0_7' in the main
       toolshed:
       https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
  -->
  <package name="bx_python" version="0.7.1">
    <install version="1.0">
      <actions>
        <action type="setup_virtualenv">
numpy==1.7.1
bx-python==0.7.1
        </action>
        <action type="set_environment">
          <environment_variable action="set_to" name="BX_PYTHON_PATH">$INSTALL_DIR</environment_variable>
        </action>
      </actions>
    </install>
    <readme>
      Installation of bx-python 0.7.1 along with numpy 1.7.1. The installation can be
      accessed via BX_PYTHON_PATH.
    </readme>
  </package>
  <!-- cistrome_ceas
       Installs the version of CEAS package found in the Cistrome
       distribution:
       https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
  -->
  <package name="cistrome_ceas" version="1.0.2.d8c0751">
    <install version="1.0">
      <actions>
	<action type="shell_command">
	  hg clone https://bitbucket.org/cistrome/cistrome-applications-harvard cistrome_ceas
	</action>
	<action type="shell_command">
	  hg update d8c0751
	</action>
        <action type="make_directory">$INSTALL_DIR/lib/python</action>
        <action type="shell_command">
	  cd published-packages/CEAS/
          export PYTHONPATH=$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>Installs version 1.0.2 of CEAS from cistrome (commit id d8c0751,
    datestamp 20140929), which includes ceasBW (a version of ceas which can
    handle bigWig file input from MACS2.

    Cistrome code is at
    https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
      
    The CEAS code is under the published-packages/CEAS/ subdirectory

    Cistrome data files and documentation can be found at
    http://liulab.dfci.harvard.edu/CEAS/index.html
    </readme>
  </package>
  <!-- fetchChromSize from UCSC tools -->
  <package name="ucsc_fetchChromSizes" version="1.0">
      <install version="1.0">
        <actions>
          <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">$INSTALL_DIR/fetchChromSizes</file>
          </action>
          <action type="set_environment">
            <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
        </action>
	</actions>
      </install>
    <readme>Installs the binary executable for the fetchChromSizes utility
    from UCSC tools
    </readme>
  </package>
</tool_dependency>