Mercurial > repos > wolma > mimodd

comparison tool_dependencies.xml @ 0:6231ae8f87b8

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author wolma
date Wed, 11 Feb 2015 08:29:02 -0500
parents
children ffee8534a5c4
comparison
equal deleted inserted replaced
-1:000000000000 0:6231ae8f87b8
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
10 <package name="mimodd" version="0.1.5.2">
11 <install version="1.0">
12 <actions>
13 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.5.2.tar.gz</action>
14 <action type="set_environment_for_install">
15 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
16 <package name="python3" version="3.4.1" />
17 </repository>
18 </action>
19 <action type="set_environment_for_install">
20 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
21 <package name="zlib" version="1.2.8" />
22 </repository>
23 </action>
24 <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action>
25 <!-- remove the plain python symlink from the venv to avoid its
26 accidental use by Galaxy, MiModD uses python3 explicitly -->
27 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
28 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
29 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
30 <!-- make MiModD's wrapped binaries executable -->
31 <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action>
32
33
34 <action type="set_environment">
35 <!-- make the mimodd entry script discoverable -->
36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
37 <!-- clear $PYTHONPATH and $PYTHONHOME -->
38 <environment_variable action="set_to" name="PYTHONPATH" />
39 <environment_variable action="set_to" name="PYTHONHOME" />
40 <!-- propagate $LD_LIBRARY_PATH -->
41 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
42 </action>
43
44
45 </actions>
46 </install>
47 <readme>
48 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
49 Home-page: http://sourceforge.net/projects/mimodd/
50 Author: Wolfgang Maier
51 Author-email: wolfgang.maier@biologie.uni-freiburg.de
52 License: GPL
53 Download-URL: http://sourceforge.net/projects/mimodd/
54
55 MiModD - Identify Mutations from Whole-Genome Sequencing Data
56 *************************************************************
57
58 MiModD is an integrated solution for efficient and user-friendly analysis of
59 whole-genome sequencing (WGS) data from laboratory model organisms.
60 It enables geneticists to identify the genetic mutations present in an organism
61 starting from just raw WGS read data and a reference genome without the help of
62 a trained bioinformatician.
63
64 MiModD is designed for good performance on standard hardware and enables WGS
65 data analysis for most model organisms on regular desktop PCs.
66
67 MiModD can be installed under Linux and Mac OS with minimal software
68 requirements and a simple setup procedure. As a standalone package it can be
69 used from the command line, but can also be integrated seamlessly and easily
70 into any local installation of a Galaxy bioinformatics server providing a
71 graphical user interface, database management of results and simple composition
72 of analysis steps into workflows.
73 </readme>
74 </package>
75 </tool_dependency>