annotate tool_dependencies.xml @ 24:3accdbe6503b draft default tip

Deleted selected files

<?xml version="1.0"?>
<tool_dependency>
  <package name="zlib" version="1.2.8">
    <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="R" version="3.2.1">
    <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="readline" version="6.3">
    <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="python3" version="3.4">
    <repository changeset_revision="83407422ec16" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
    
  <package name="mimodd" version="0.1.7.3">
    <install version="1.0">
      <actions>
      <!-- prepare a python3 venv to install into -->
        <action type="set_environment_for_install">
          <repository changeset_revision="83407422ec16" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
            <package name="python3" version="3.4" />
          </repository>
        </action>
        <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action>
        <!-- remove the plain python symlink from the venv to avoid its 
             accidental use by Galaxy, MiModD uses python3 explicitly -->
        <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>

      <!-- download and install setuptools (required to install rpy2) -->
        <action type="change_directory">$TMP_WORK_DIR</action>
        <action sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25" type="download_file">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action>
        <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action>
        <action type="change_directory">pypa-setuptools-1a981f2e5031</action>
        <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>

      <!-- download and install six (required by rpy2) -->
        <action type="change_directory">$TMP_WORK_DIR</action>
        <action sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5" type="download_file">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action>
        <action type="shell_command">tar -xzf six_1.9.0_src_all.tar.gz</action>
        <action type="change_directory">six-1.9.0</action>
        <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>

      <!-- download and install rpy2 -->
        <action type="change_directory">$TMP_WORK_DIR</action>
        <action sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441" type="download_file">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action>
        <action type="shell_command">tar -xzf rpy2_2.7.5_src_all.tar.gz</action>
        <action type="change_directory">rpy2-2.7.5</action>
        <action type="set_environment_for_install">
          <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
            <package name="readline" version="6.3" />
          </repository>
          <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
            <package name="R" version="3.2.1" />
          </repository>
        </action>
        <action type="shell_command">
          export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp;
          export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp;
          $INSTALL_DIR/MiModD_venv/bin/python3 setup.py install
        </action>

      <!-- download and install MiModD -->
        <action type="change_directory">$TMP_WORK_DIR</action>
        <action type="download_file">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.3/MiModD-0.1.7.3.tar.gz</action>
        <action type="shell_command">tar -xzf MiModD-0.1.7.3.tar.gz</action>
        <action type="change_directory">MiModD-0.1.7.3</action>
        <action type="set_environment_for_install">
          <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
            <package name="zlib" version="1.2.8" />
          </repository>
        </action>
        <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
        <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
        <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
        <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action>
        
      <!-- configure environment -->
        <action type="set_environment">
          <!-- since the iuc R package does not export the path to R's libR.so,
               any venv using rpy2, needs to record this path -->
          <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[R_HOME]/lib</environment_variable>
          <!-- to make MiModD accessible it is sufficient to simply add the 
               venvs site-packages directory to PYTHONPATH; 
               SITE_PACKAGES_RELPATH will be made available by the python3 
               package, which all MiModD toolwrappers require -->
          <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/MiModD_venv/$SITE_PACKAGES_RELPATH</environment_variable>
        </action>
      </actions>
    </install>
    
    <readme>
Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
Home-page: http://sourceforge.net/projects/mimodd/
Author: Wolfgang Maier
Author-email: [e-mail]
License: GPL
Download-URL: http://sourceforge.net/projects/mimodd/

MiModD - Identify Mutations from Whole-Genome Sequencing Data
*************************************************************
        
MiModD is an integrated solution for efficient and user-friendly analysis of 
whole-genome sequencing (WGS) data from laboratory model organisms. 
It enables geneticists to identify the genetic mutations present in an organism 
starting from just raw WGS read data and a reference genome without the help of 
a trained bioinformatician.

MiModD is designed for good performance on standard hardware and enables WGS 
data analysis for most model organisms on regular desktop PCs.

Detailed documentation of the software can be found at:

  http://mimodd.readthedocs.io

    </readme>
  </package>
</tool_dependency>