annotate tool_dependencies.xml @ 19:8f108b41a149 draft

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author wolma
date Tue, 26 Apr 2016 15:27:13 -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="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" 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="6.3">
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10 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" 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">
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13 <repository changeset_revision="3956f4688295" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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14 </package>
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93db2f9bca12 upgrade to v0.1.7.2
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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="3956f4688295" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
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22 <package name="python3" version="3.4" />
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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 $INSTALL_DIR/MiModD_venv/bin/python</action>
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29
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30 <!-- download and install setuptools (required to install rpy2) -->
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31 <action type="download_file" sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action>
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32 <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action>
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33 <action type="change_directory">pypa-setuptools-1a981f2e5031</action>
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34 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
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35 <action type="change_directory">$TMP_WORK_DIR</action>
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36
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37 <!-- download and install six (required by rpy2) -->
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38 <action type="download_file" sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action>
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39 <action type="shell_command">tar -xzf six_1.9.0_src_all.tar.gz</action>
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40 <action type="change_directory">six-1.9.0</action>
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41 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
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42 <action type="change_directory">$TMP_WORK_DIR</action>
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43
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44 <!-- download and install rpy2 -->
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45 <action type="download_file" sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action>
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46 <action type="shell_command">tar -xzf rpy2_2.7.5_src_all.tar.gz</action>
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47 <action type="change_directory">rpy2-2.7.5</action>
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48 <action type="set_environment_for_install">
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49 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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50 <package name="readline" version="6.3" />
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51 </repository>
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52 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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53 <package name="R" version="3.2.1" />
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54 </repository>
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55 </action>
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56 <action type="shell_command">
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57 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp;
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58 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp;
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59 $INSTALL_DIR/MiModD_venv/bin/python3 setup.py install
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60 </action>
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61 <action type="change_directory">$TMP_WORK_DIR</action>
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62
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63 <!-- download and install MiModD -->
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64 <action type="download_file">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action>
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65 <action type="shell_command">tar -xzf MiModD-0.1.7.2.tar.gz</action>
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66 <action type="change_directory">MiModD-0.1.7.2</action>
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67 <action type="set_environment_for_install">
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68 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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69 <package name="zlib" version="1.2.8" />
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70 </repository>
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71 </action>
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72 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
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73 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
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74 <!-- make MiModD's wrapped binaries executable -->
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75 <action type="chmod"><file mode="755">$INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</file></action>
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76 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
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77 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action>
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79 <action type="set_environment">
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80 <!-- make the mimodd entry script discoverable -->
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81 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
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82 <!-- clear $PYTHONPATH and $PYTHONHOME -->
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83 <environment_variable action="set_to" name="PYTHONPATH" />
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84 <environment_variable action="set_to" name="PYTHONHOME" />
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85 <!-- propagate $LD_LIBRARY_PATH -->
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86 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
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87 </action>
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88
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89 </actions>
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90 </install>
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91 <readme>
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92 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
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93 Home-page: http://sourceforge.net/projects/mimodd/
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94 Author: Wolfgang Maier
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95 Author-email: wolfgang.maier@biologie.uni-freiburg.de
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96 License: GPL
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97 Download-URL: http://sourceforge.net/projects/mimodd/
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98
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99 MiModD - Identify Mutations from Whole-Genome Sequencing Data
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100 *************************************************************
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101
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102 MiModD is an integrated solution for efficient and user-friendly analysis of
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103 whole-genome sequencing (WGS) data from laboratory model organisms.
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104 It enables geneticists to identify the genetic mutations present in an organism
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105 starting from just raw WGS read data and a reference genome without the help of
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106 a trained bioinformatician.
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107
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108 MiModD is designed for good performance on standard hardware and enables WGS
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109 data analysis for most model organisms on regular desktop PCs.
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110
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111 MiModD can be installed under Linux and Mac OS with minimal software
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112 requirements and a simple setup procedure. As a standalone package it can be
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113 used from the command line, but can also be integrated seamlessly and easily
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114 into any local installation of a Galaxy bioinformatics server providing a
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115 graphical user interface, database management of results and simple composition
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116 of analysis steps into workflows.
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117 </readme>
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118 </package>
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119 </tool_dependency>