|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3 <package name="zlib" version="1.2.8">
|
|
2
|
4 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
|
|
1
|
5 </package>
|
|
|
6 <package name="python3" version="3.4.1">
|
|
2
|
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" />
|
|
1
|
8 </package>
|
|
|
9
|
|
|
10 <package name="mimodd" version="0.1.5">
|
|
|
11 <install version="1.0">
|
|
|
12 <actions>
|
|
|
13 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.5.1.tar.gz</action>
|
|
|
14 <action type="set_environment_for_install">
|
|
2
|
15 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
|
|
1
|
16 <package name="python3" version="3.4.1" />
|
|
|
17 </repository>
|
|
|
18 </action>
|
|
|
19 <action type="set_environment_for_install">
|
|
2
|
20 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
|
|
1
|
21 <package name="zlib" version="1.2.8" />
|
|
|
22 </repository>
|
|
|
23 </action>
|
|
|
24 <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action>
|
|
|
25 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
|
|
|
26 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
|
|
|
27 <!-- make MiModD's wrapped binaries executable -->
|
|
|
28 <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action>
|
|
|
29
|
|
|
30
|
|
|
31 <action type="set_environment">
|
|
|
32 <!-- make the mimodd entry script discoverable -->
|
|
|
33 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
|
|
|
34 <!-- clear $PYTHONPATH and $PYTHONHOME -->
|
|
|
35 <environment_variable action="set_to" name="PYTHONPATH" />
|
|
|
36 <environment_variable action="set_to" name="PYTHONHOME" />
|
|
|
37 <!-- propagate $LD_LIBRARY_PATH -->
|
|
|
38 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
|
|
|
39 </action>
|
|
|
40
|
|
|
41
|
|
|
42 </actions>
|
|
|
43 </install>
|
|
|
44 <readme>
|
|
0
|
45 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
|
|
|
46 Home-page: http://sourceforge.net/projects/mimodd/
|
|
|
47 Author: Wolfgang Maier
|
|
|
48 Author-email: wolfgang.maier@biologie.uni-freiburg.de
|
|
|
49 License: GPL
|
|
|
50 Download-URL: http://sourceforge.net/projects/mimodd/
|
|
|
51
|
|
|
52 MiModD - Identify Mutations from Whole-Genome Sequencing Data
|
|
|
53 *************************************************************
|
|
|
54
|
|
|
55 MiModD is an integrated solution for efficient and user-friendly analysis of
|
|
|
56 whole-genome sequencing (WGS) data from laboratory model organisms.
|
|
|
57 It enables geneticists to identify the genetic mutations present in an organism
|
|
|
58 starting from just raw WGS read data and a reference genome without the help of
|
|
|
59 a trained bioinformatician.
|
|
|
60
|
|
|
61 MiModD is designed for good performance on standard hardware and enables WGS
|
|
|
62 data analysis for most model organisms on regular desktop PCs.
|
|
|
63
|
|
|
64 MiModD can be installed under Linux and Mac OS with minimal software
|
|
|
65 requirements and a simple setup procedure. As a standalone package it can be
|
|
|
66 used from the command line, but can also be integrated seamlessly and easily
|
|
|
67 into any local installation of a Galaxy bioinformatics server providing a
|
|
|
68 graphical user interface, database management of results and simple composition
|
|
|
69 of analysis steps into workflows.
|
|
|
70 </readme>
|
|
1
|
71 </package>
|
|
0
|
72 </tool_dependency>
|
