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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="zlib" version="1.2.8">
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4 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="python3" version="3.4.1">
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7 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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8 </package>
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9
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10 <package name="mimodd" version="0.1.5.2">
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11 <install version="1.0">
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12 <actions>
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13 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.5.2.tar.gz</action>
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14 <action type="set_environment_for_install">
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15 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
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16 <package name="python3" version="3.4.1" />
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17 </repository>
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18 </action>
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19 <action type="set_environment_for_install">
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20 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
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21 <package name="zlib" version="1.2.8" />
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22 </repository>
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23 </action>
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24 <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action>
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25 <!-- remove the plain python symlink from the venv to avoid its
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26 accidental use by Galaxy, MiModD uses python3 explicitly -->
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27 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
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28 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
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29 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
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30 <!-- make MiModD's wrapped binaries executable -->
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31 <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action>
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32
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33
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34 <action type="set_environment">
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35 <!-- make the mimodd entry script discoverable -->
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36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
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37 <!-- clear $PYTHONPATH and $PYTHONHOME -->
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38 <environment_variable action="set_to" name="PYTHONPATH" />
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39 <environment_variable action="set_to" name="PYTHONHOME" />
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40 <!-- propagate $LD_LIBRARY_PATH -->
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41 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
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42 </action>
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43
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44
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45 </actions>
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46 </install>
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47 <readme>
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48 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
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49 Home-page: http://sourceforge.net/projects/mimodd/
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50 Author: Wolfgang Maier
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51 Author-email: wolfgang.maier@biologie.uni-freiburg.de
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52 License: GPL
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53 Download-URL: http://sourceforge.net/projects/mimodd/
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54
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55 MiModD - Identify Mutations from Whole-Genome Sequencing Data
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56 *************************************************************
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57
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58 MiModD is an integrated solution for efficient and user-friendly analysis of
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59 whole-genome sequencing (WGS) data from laboratory model organisms.
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60 It enables geneticists to identify the genetic mutations present in an organism
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61 starting from just raw WGS read data and a reference genome without the help of
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62 a trained bioinformatician.
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63
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64 MiModD is designed for good performance on standard hardware and enables WGS
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65 data analysis for most model organisms on regular desktop PCs.
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66
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67 MiModD can be installed under Linux and Mac OS with minimal software
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68 requirements and a simple setup procedure. As a standalone package it can be
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69 used from the command line, but can also be integrated seamlessly and easily
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70 into any local installation of a Galaxy bioinformatics server providing a
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71 graphical user interface, database management of results and simple composition
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72 of analysis steps into workflows.
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73 </readme>
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74 </package>
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75 </tool_dependency>
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