annotate tool_dependencies.xml @ 13:f0b3871cb869 draft

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author wolma
date Mon, 25 Apr 2016 17:27:25 -0400
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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="R" version="3.2.1">
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7 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="readline" version="6.2">
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10 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="python3" version="3.4.1">
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13 <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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14 </package>
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15
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16 <package name="mimodd" version="0.1.7.2">
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17 <install version="1.0">
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18 <actions>
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19 <!-- prepare a python3 venv to install into -->
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20 <action type="set_environment_for_install">
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21 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
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22 <package name="python3" version="3.4.1" />
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23 </repository>
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24 </action>
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25 <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action>
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26 <!-- remove the plain python symlink from the venv to avoid its
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27 accidental use by Galaxy, MiModD uses python3 explicitly -->
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28 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
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29 <action type="shell_command">. $INSTALL_DIR/MiModD_venv/bin/activate</action>
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30
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31 <!-- download and install rpy2 -->
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32 <action sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441" type="download_by_url">
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33 https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz
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34 </action>
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35 <action type="set_environment_for_install">
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36 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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37 <package name="readline" version="6.2" />
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38 </repository>
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39 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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40 <package name="R" version="3.2.1" />
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41 </repository>
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42 </action>
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43 <action type="shell_command">
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44 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp;
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45 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp;
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46 python3 setup.py install
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47 </action>
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48 <action type="change_directory">$TMP_WORK_DIR</action>
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49
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50 <!-- download and install MiModD -->
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51 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action>
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52 <action type="set_environment_for_install">
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53 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
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54 <package name="zlib" version="1.2.8" />
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55 </repository>
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56 </action>
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57 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
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58 <action type="shell_command">python3 setup.py install</action>
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59 <!-- make MiModD's wrapped binaries executable -->
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60 <action type="chmod"><file mode="755">$INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</file></action>
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61 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
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62 <action type="shell_command">python3 -m MiModD.__first_run__</action>
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63
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64 <action type="set_environment">
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65 <!-- make the mimodd entry script discoverable -->
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66 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
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67 <!-- clear $PYTHONPATH and $PYTHONHOME -->
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68 <environment_variable action="set_to" name="PYTHONPATH" />
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69 <environment_variable action="set_to" name="PYTHONHOME" />
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70 <!-- propagate $LD_LIBRARY_PATH -->
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71 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
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72 </action>
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73
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74 </actions>
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75 </install>
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76 <readme>
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77 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
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78 Home-page: http://sourceforge.net/projects/mimodd/
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79 Author: Wolfgang Maier
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80 Author-email: wolfgang.maier@biologie.uni-freiburg.de
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81 License: GPL
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82 Download-URL: http://sourceforge.net/projects/mimodd/
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83
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84 MiModD - Identify Mutations from Whole-Genome Sequencing Data
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85 *************************************************************
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86
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87 MiModD is an integrated solution for efficient and user-friendly analysis of
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88 whole-genome sequencing (WGS) data from laboratory model organisms.
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89 It enables geneticists to identify the genetic mutations present in an organism
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90 starting from just raw WGS read data and a reference genome without the help of
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91 a trained bioinformatician.
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92
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93 MiModD is designed for good performance on standard hardware and enables WGS
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94 data analysis for most model organisms on regular desktop PCs.
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95
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96 MiModD can be installed under Linux and Mac OS with minimal software
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97 requirements and a simple setup procedure. As a standalone package it can be
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98 used from the command line, but can also be integrated seamlessly and easily
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99 into any local installation of a Galaxy bioinformatics server providing a
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100 graphical user interface, database management of results and simple composition
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101 of analysis steps into workflows.
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102 </readme>
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103 </package>
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104 </tool_dependency>