annotate tool_dependencies.xml @ 9:93db2f9bca12

upgrade to v0.1.7.2
author Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
date Thu, 28 Jan 2016 17:26:58 +0100
parents d79fe626c6fd
children ac3eac581b83
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
1 <?xml version="1.0"?>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
2 <tool_dependency>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
3 <package name="zlib" version="1.2.8">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
4 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
5 </package>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
6 <package name="python3" version="3.4.1">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
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" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
8 </package>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
9
9
93db2f9bca12 upgrade to v0.1.7.2
Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
parents: 8
diff changeset
10 <package name="mimodd" version="0.1.7.2">
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
11 <install version="1.0">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
12 <actions>
8
d79fe626c6fd upgrade to v0.1.7.1
Wolfgang Maier
parents: 7
diff changeset
13 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.1.tar.gz</action>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
14 <action type="set_environment_for_install">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
15 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
16 <package name="python3" version="3.4.1" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
17 </repository>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
18 </action>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
19 <action type="set_environment_for_install">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
20 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
21 <package name="zlib" version="1.2.8" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
22 </repository>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
23 </action>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
24 <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
25 <!-- remove the plain python symlink from the venv to avoid its
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
26 accidental use by Galaxy, MiModD uses python3 explicitly -->
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
27 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
28 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
29 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
30 <!-- make MiModD's wrapped binaries executable -->
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
31 <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action>
7
3619e85a5477 v0.1.7.0 bug fixes
Wolfgang Maier
parents: 6
diff changeset
32 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
3619e85a5477 v0.1.7.0 bug fixes
Wolfgang Maier
parents: 6
diff changeset
33 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action>
3619e85a5477 v0.1.7.0 bug fixes
Wolfgang Maier
parents: 6
diff changeset
34
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
35 <action type="set_environment">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
36 <!-- make the mimodd entry script discoverable -->
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
37 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
38 <!-- clear $PYTHONPATH and $PYTHONHOME -->
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
39 <environment_variable action="set_to" name="PYTHONPATH" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
40 <environment_variable action="set_to" name="PYTHONHOME" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
41 <!-- propagate $LD_LIBRARY_PATH -->
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
42 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
43 </action>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
44
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
45
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
46 </actions>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
47 </install>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
48 <readme>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
49 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
50 Home-page: http://sourceforge.net/projects/mimodd/
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
51 Author: Wolfgang Maier
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
52 Author-email: wolfgang.maier@biologie.uni-freiburg.de
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
53 License: GPL
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
54 Download-URL: http://sourceforge.net/projects/mimodd/
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
55
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
56 MiModD - Identify Mutations from Whole-Genome Sequencing Data
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
57 *************************************************************
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
58
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
59 MiModD is an integrated solution for efficient and user-friendly analysis of
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
60 whole-genome sequencing (WGS) data from laboratory model organisms.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
61 It enables geneticists to identify the genetic mutations present in an organism
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
62 starting from just raw WGS read data and a reference genome without the help of
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
63 a trained bioinformatician.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
64
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
65 MiModD is designed for good performance on standard hardware and enables WGS
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
66 data analysis for most model organisms on regular desktop PCs.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
67
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
68 MiModD can be installed under Linux and Mac OS with minimal software
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
69 requirements and a simple setup procedure. As a standalone package it can be
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
70 used from the command line, but can also be integrated seamlessly and easily
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
71 into any local installation of a Galaxy bioinformatics server providing a
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
72 graphical user interface, database management of results and simple composition
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
73 of analysis steps into workflows.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
74 </readme>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
75 </package>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
76 </tool_dependency>