annotate tool_dependencies.xml @ 19:8f108b41a149 draft

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<?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="d0bf97420fb5" 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="3956f4688295" 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="0.1.7.2">
    <install version="1.0">
      <actions>
      <!-- prepare a python3 venv to install into -->
        <action type="set_environment_for_install">
          <repository changeset_revision="3956f4688295" 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="download_file" sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25">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">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
        <action type="change_directory">$TMP_WORK_DIR</action>

      <!-- download and install six (required by rpy2) -->
        <action type="download_file" sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5">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">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
        <action type="change_directory">$TMP_WORK_DIR</action>

      <!-- download and install rpy2 -->
        <action type="download_file" sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441">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="d0bf97420fb5" 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;
          $INSTALL_DIR/MiModD_venv/bin/python3 setup.py install
        </action>
        <action type="change_directory">$TMP_WORK_DIR</action>

      <!-- download and install MiModD -->
        <action type="download_file">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action>
        <action type="shell_command">tar -xzf MiModD-0.1.7.2.tar.gz</action>
        <action type="change_directory">MiModD-0.1.7.2</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">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
      <!-- make MiModD's wrapped binaries executable -->
        <action type="chmod"><file mode="755">$INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</file></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>
                
        <action type="set_environment">
      <!-- make the mimodd entry script discoverable -->
          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
      <!-- clear $PYTHONPATH and $PYTHONHOME -->
          <environment_variable action="set_to" name="PYTHONPATH" />
          <environment_variable action="set_to" name="PYTHONHOME" />
      <!-- propagate $LD_LIBRARY_PATH -->    
          <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</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.

MiModD can be installed under Linux and Mac OS with minimal software 
requirements and a simple setup procedure. As a standalone package it can be 
used from the command line, but can also be integrated seamlessly and easily 
into any local installation of a Galaxy bioinformatics server providing a 
graphical user interface, database management of results and simple composition 
of analysis steps into workflows.
    </readme>
  </package>
</tool_dependency>