annotate tool_dependencies.xml @ 22:24154c580718 draft

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author wolma
date Sun, 12 Jun 2016 07:39:46 -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="d9f7d84125b7" 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="83407422ec16" 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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Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
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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="83407422ec16" 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 $INSTALL_DIR/MiModD_venv/bin/python</action>
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29
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30 <!-- download and install setuptools (required to install rpy2) -->
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31 <action type="change_directory">$TMP_WORK_DIR</action>
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32 <action sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25" type="download_file">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action>
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33 <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action>
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34 <action type="change_directory">pypa-setuptools-1a981f2e5031</action>
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35 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
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37 <!-- download and install six (required by rpy2) -->
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38 <action type="change_directory">$TMP_WORK_DIR</action>
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39 <action sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5" type="download_file">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action>
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40 <action type="shell_command">tar -xzf six_1.9.0_src_all.tar.gz</action>
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41 <action type="change_directory">six-1.9.0</action>
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42 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
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43
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44 <!-- download and install rpy2 -->
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45 <action type="change_directory">$TMP_WORK_DIR</action>
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46 <action sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441" type="download_file">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action>
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47 <action type="shell_command">tar -xzf rpy2_2.7.5_src_all.tar.gz</action>
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48 <action type="change_directory">rpy2-2.7.5</action>
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49 <action type="set_environment_for_install">
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50 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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51 <package name="readline" version="6.3" />
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52 </repository>
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53 <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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54 <package name="R" version="3.2.1" />
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55 </repository>
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56 </action>
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57 <action type="shell_command">
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58 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp;
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59 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp;
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60 $INSTALL_DIR/MiModD_venv/bin/python3 setup.py install
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61 </action>
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62
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63 <!-- download and install MiModD -->
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64 <action type="change_directory">$TMP_WORK_DIR</action>
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65 <action type="download_file">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action>
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66 <action type="shell_command">tar -xzf MiModD-0.1.7.2.tar.gz</action>
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67 <action type="change_directory">MiModD-0.1.7.2</action>
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68 <action type="set_environment_for_install">
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69 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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70 <package name="zlib" version="1.2.8" />
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71 </repository>
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72 </action>
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73 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
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74 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
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75 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
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76 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action>
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78 <!-- configure environment -->
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79 <action type="set_environment">
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80 <!-- since the iuc R package does not export the path to R's libR.so,
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81 any venv using rpy2, needs to record this path -->
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82 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[R_HOME]/lib</environment_variable>
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83 <!-- to make MiModD accessible it is sufficient to simply add the
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84 venvs site-packages directory to PYTHONPATH;
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85 SITE_PACKAGES_RELPATH will be made available by the python3
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86 package, which all MiModD toolwrappers require -->
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87 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/MiModD_venv/$SITE_PACKAGES_RELPATH</environment_variable>
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88 </action>
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89 </actions>
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90 </install>
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91
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92 <readme>
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93 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
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94 Home-page: http://sourceforge.net/projects/mimodd/
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95 Author: Wolfgang Maier
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96 Author-email: wolfgang.maier@biologie.uni-freiburg.de
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97 License: GPL
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98 Download-URL: http://sourceforge.net/projects/mimodd/
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99
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100 MiModD - Identify Mutations from Whole-Genome Sequencing Data
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101 *************************************************************
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102
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103 MiModD is an integrated solution for efficient and user-friendly analysis of
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104 whole-genome sequencing (WGS) data from laboratory model organisms.
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105 It enables geneticists to identify the genetic mutations present in an organism
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106 starting from just raw WGS read data and a reference genome without the help of
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107 a trained bioinformatician.
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108
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109 MiModD is designed for good performance on standard hardware and enables WGS
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110 data analysis for most model organisms on regular desktop PCs.
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111
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112 Detailed documentation of the software can be found at:
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113
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114 http://mimodd.readthedocs.io
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115
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116 </readme>
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117 </package>
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118 </tool_dependency>