Mercurial > repos > jjohnson > package_cistrome_2014_09_29

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Imported from capsule None
author jjohnson
date Tue, 14 Oct 2014 10:06:50 -0400
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<?xml version="1.0"?>
<tool_dependency>
  <package name="numpy" version="1.7.1">
      <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="cython" version="0.20.1">
      <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="cistrome" version="2014-09-29">
      <install version="1.0">
          <actions>
              <action type="shell_command">hg clone https://bitbucket.org/jjohnson/cistrome-applications-harvard cistrome</action>
                <action type="shell_command">hg update -d 2014-09-29</action>
                <action type="shell_command">cd cistrome-extra-apps &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
                <action type="shell_command">cd published-packages/CEAS &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
                <action type="shell_command">cd published-packages/MA2C &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
                <!--  needs numpy  -->
                <action type="set_environment_for_install">
                  <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                      <package name="numpy" version="1.7.1" />
                    </repository>
                </action>
                <action type="shell_command">cd published-packages/MACS &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
                <action type="shell_command">cd published-packages/MAT &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
                <action type="shell_command">cd published-packages/NPS &amp;&amp; python setup.py install --home=$INSTALL_DIR</action>
                <!--  needs numpy Cython  -->
                <action type="set_environment_for_install">
                  <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                      <package name="cython" version="0.20.1" />
                    </repository>
                </action>
                <action type="shell_command">
                   export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
                   cd mdseqpos &amp;&amp; 
                   sed "s#/data/static_libraries/assembly/#$INSTALL_DIR/assembly/#" lib/settings.py.example &gt; lib/settings.py &amp;&amp; 
                   sed -i".tmp" "s#NUMPY_PATH = numpy#global NUMPY_PATH; NUMPY_PATH = numpy#" setup.py  &amp;&amp;
                   python setup.py install --home=$INSTALL_DIR
                </action>
                <action type="set_environment">
                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
                <!--  this includes CistromeAP  -->
                <action type="set_environment">
                  <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib64/python</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
Installs the cistrome applications code from https://bitbucket.org/cistrome/cistrome-applications-harvard
  ( branch for genome_dir option to override settings.py  https://bitbucket.org/jjohnson/cistrome-applications-harvard )
Runtime dependencies: bx-python, biopython, PIL, jinja2, MySQLdb
        </readme>
    </package>
</tool_dependency>