Mercurial > repos > wolma > mimodd

comparison tool_dependencies.xml @ 20:aba6d9b1c1f1 draft

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author wolma
date Fri, 29 Apr 2016 06:01:46 -0400
parents 8f108b41a149
children c46406466625
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19:8f108b41a149 20:aba6d9b1c1f1
8 </package> 8 </package>
9 <package name="readline" version="6.3"> 9 <package name="readline" version="6.3">
10 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="python3" version="3.4"> 12 <package name="python3" version="3.4">
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" /> 13 <repository changeset_revision="5e5653b689ca" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 15
16 <package name="mimodd" version="0.1.7.2"> 16 <package name="mimodd" version="0.1.7.2">
17 <install version="1.0"> 17 <install version="1.0">
18 <actions> 18 <actions>
19 <!-- prepare a python3 venv to install into --> 19 <!-- prepare a python3 venv to install into -->
20 <action type="set_environment_for_install"> 20 <action type="set_environment_for_install">
21 <repository changeset_revision="3956f4688295" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> 21 <repository changeset_revision="5e5653b689ca" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
22 <package name="python3" version="3.4" /> 22 <package name="python3" version="3.4" />
23 </repository> 23 </repository>
24 </action> 24 </action>
25 <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action> 25 <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action>
26 <!-- remove the plain python symlink from the venv to avoid its 26 <!-- remove the plain python symlink from the venv to avoid its
27 accidental use by Galaxy, MiModD uses python3 explicitly --> 27 accidental use by Galaxy, MiModD uses python3 explicitly -->
28 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action> 28 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
29 29
30 <!-- download and install setuptools (required to install rpy2) --> 30 <!-- download and install setuptools (required to install rpy2) -->
31 <action type="download_file" sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action> 31 <action type="change_directory">$TMP_WORK_DIR</action>
32 <action sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25" type="download_file">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action>
32 <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action> 33 <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action>
33 <action type="change_directory">pypa-setuptools-1a981f2e5031</action> 34 <action type="change_directory">pypa-setuptools-1a981f2e5031</action>
34 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action> 35 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
35 <action type="change_directory">$TMP_WORK_DIR</action>
36 36
37 <!-- download and install six (required by rpy2) --> 37 <!-- download and install six (required by rpy2) -->
38 <action type="download_file" sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action> 38 <action type="change_directory">$TMP_WORK_DIR</action>
39 <action sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5" type="download_file">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action>
39 <action type="shell_command">tar -xzf six_1.9.0_src_all.tar.gz</action> 40 <action type="shell_command">tar -xzf six_1.9.0_src_all.tar.gz</action>
40 <action type="change_directory">six-1.9.0</action> 41 <action type="change_directory">six-1.9.0</action>
41 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action> 42 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
42 <action type="change_directory">$TMP_WORK_DIR</action>
43 43
44 <!-- download and install rpy2 --> 44 <!-- download and install rpy2 -->
45 <action type="download_file" sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action> 45 <action type="change_directory">$TMP_WORK_DIR</action>
46 <action sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441" type="download_file">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action>
46 <action type="shell_command">tar -xzf rpy2_2.7.5_src_all.tar.gz</action> 47 <action type="shell_command">tar -xzf rpy2_2.7.5_src_all.tar.gz</action>
47 <action type="change_directory">rpy2-2.7.5</action> 48 <action type="change_directory">rpy2-2.7.5</action>
48 <action type="set_environment_for_install"> 49 <action type="set_environment_for_install">
49 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 50 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
50 <package name="readline" version="6.3" /> 51 <package name="readline" version="6.3" />
56 <action type="shell_command"> 57 <action type="shell_command">
57 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp; 58 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp;
58 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp; 59 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp;
59 $INSTALL_DIR/MiModD_venv/bin/python3 setup.py install 60 $INSTALL_DIR/MiModD_venv/bin/python3 setup.py install
60 </action> 61 </action>
61 <action type="change_directory">$TMP_WORK_DIR</action>
62 62
63 <!-- download and install MiModD --> 63 <!-- download and install MiModD -->
64 <action type="change_directory">$TMP_WORK_DIR</action>
64 <action type="download_file">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action> 65 <action type="download_file">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action>
65 <action type="shell_command">tar -xzf MiModD-0.1.7.2.tar.gz</action> 66 <action type="shell_command">tar -xzf MiModD-0.1.7.2.tar.gz</action>
66 <action type="change_directory">MiModD-0.1.7.2</action> 67 <action type="change_directory">MiModD-0.1.7.2</action>
67 <action type="set_environment_for_install"> 68 <action type="set_environment_for_install">
68 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 69 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
69 <package name="zlib" version="1.2.8" /> 70 <package name="zlib" version="1.2.8" />
70 </repository> 71 </repository>
71 </action> 72 </action>
72 <!-- install MiModD placing the entry script mimodd into the venv's bin directory --> 73 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
73 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action> 74 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
74 <!-- make MiModD's wrapped binaries executable --> 75 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
75 <action type="chmod"><file mode="755">$INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</file></action>
76 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
77 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action> 76 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action>
78 77
78 <!-- configure environment -->
79 <action type="set_environment"> 79 <action type="set_environment">
80 <!-- make the mimodd entry script discoverable --> 80 <!-- make the mimodd entry script discoverable -->
81 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable> 81 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
82 <!-- clear $PYTHONPATH and $PYTHONHOME -->
83 <environment_variable action="set_to" name="PYTHONPATH" />
84 <environment_variable action="set_to" name="PYTHONHOME" />
85 <!-- propagate $LD_LIBRARY_PATH -->
86 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
87 </action> 82 </action>
88
89 </actions> 83 </actions>
90 </install> 84 </install>
85
91 <readme> 86 <readme>
92 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs 87 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
93 Home-page: http://sourceforge.net/projects/mimodd/ 88 Home-page: http://sourceforge.net/projects/mimodd/
94 Author: Wolfgang Maier 89 Author: Wolfgang Maier
95 Author-email: wolfgang.maier@biologie.uni-freiburg.de 90 Author-email: wolfgang.maier@biologie.uni-freiburg.de
106 a trained bioinformatician. 101 a trained bioinformatician.
107 102
108 MiModD is designed for good performance on standard hardware and enables WGS 103 MiModD is designed for good performance on standard hardware and enables WGS
109 data analysis for most model organisms on regular desktop PCs. 104 data analysis for most model organisms on regular desktop PCs.
110 105
111 MiModD can be installed under Linux and Mac OS with minimal software 106 Detailed documentation of the software can be found at:
112 requirements and a simple setup procedure. As a standalone package it can be 107
113 used from the command line, but can also be integrated seamlessly and easily 108 http://mimodd.readthedocs.io
114 into any local installation of a Galaxy bioinformatics server providing a 109
115 graphical user interface, database management of results and simple composition
116 of analysis steps into workflows.
117 </readme> 110 </readme>
118 </package> 111 </package>
119 </tool_dependency> 112 </tool_dependency>