Mercurial > repos > wolma > package_mimodd_0_1_5

comparison tool_dependencies.xml @ 0:fbac402764d6 draft

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Imported from capsule None
author wolma
date Sat, 13 Dec 2014 17:19:41 -0500
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children 46fd9b9b753f
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="zlib" version="1.2.8">
4 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="python3" version="3.4.1">
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" />
8 </package>
9 <package name="mimodd" version="0.1.5">
10 <install version="1.0">
11 <actions>
12 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.5.tar.gz</action>
13 <action type="set_environment_for_install">
14 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
15 <package name="python3" version="3.4.1" />
16 </repository>
17 </action>
18 <action type="set_environment_for_install">
19 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
20 <package name="zlib" version="1.2.8" />
21 </repository>
22 </action>
23 <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action>
24 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
25 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
26 <!-- make MiModD's wrapped binaries executable -->
27 <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action>
28 <action type="set_environment">
29 <!-- make the mimodd entry script discoverable -->
30 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
31 <!-- clear $PYTHONPATH and $PYTHONHOME -->
32 <environment_variable action="set_to" name="PYTHONPATH" />
33 <environment_variable action="set_to" name="PYTHONHOME" />
34 <!-- propagate $LD_LIBRARY_PATH -->
35 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
36 </action>
37 </actions>
38 </install>
39 <readme>
40 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
41 Home-page: http://sourceforge.net/projects/mimodd/
42 Author: Wolfgang Maier
43 Author-email: wolfgang.maier@biologie.uni-freiburg.de
44 License: GPL
45 Download-URL: http://sourceforge.net/projects/mimodd/
46
47 MiModD - Identify Mutations from Whole-Genome Sequencing Data
48 *************************************************************
49
50 MiModD is an integrated solution for efficient and user-friendly analysis of
51 whole-genome sequencing (WGS) data from laboratory model organisms.
52 It enables geneticists to identify the genetic mutations present in an organism
53 starting from just raw WGS read data and a reference genome without the help of
54 a trained bioinformatician.
55
56 MiModD is designed for good performance on standard hardware and enables WGS
57 data analysis for most model organisms on regular desktop PCs.
58
59 MiModD can be installed under Linux and Mac OS with minimal software
60 requirements and a simple setup procedure. As a standalone package it can be
61 used from the command line, but can also be integrated seamlessly and easily
62 into any local installation of a Galaxy bioinformatics server providing a
63 graphical user interface, database management of results and simple composition
64 of analysis steps into workflows.
65 </readme>
66 </package>
67 </tool_dependency>