annotate tool_dependencies.xml @ 21:c46406466625 draft

Uploaded
author wolma
date Sat, 11 Jun 2016 19:10:44 -0400
parents aba6d9b1c1f1
children 24154c580718
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">
16
e676aa6997cc Uploaded
wolma
parents: 15
diff changeset
4 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
5 </package>
13
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
6 <package name="R" version="3.2.1">
21
c46406466625 Uploaded
wolma
parents: 20
diff changeset
7 <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
13
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
8 </package>
14
5e9c1c67716b Uploaded
wolma
parents: 13
diff changeset
9 <package name="readline" version="6.3">
5e9c1c67716b Uploaded
wolma
parents: 13
diff changeset
10 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
13
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
11 </package>
18
2742ad4d1608 rebase on package_python_3_4_lean
wolma
parents: 17
diff changeset
12 <package name="python3" version="3.4">
21
c46406466625 Uploaded
wolma
parents: 20
diff changeset
13 <repository changeset_revision="83407422ec16" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
14 </package>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
15
9
93db2f9bca12 upgrade to v0.1.7.2
Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
parents: 8
diff changeset
16 <package name="mimodd" version="0.1.7.2">
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
17 <install version="1.0">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
18 <actions>
13
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
19 <!-- prepare a python3 venv to install into -->
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
20 <action type="set_environment_for_install">
21
c46406466625 Uploaded
wolma
parents: 20
diff changeset
21 <repository changeset_revision="83407422ec16" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
18
2742ad4d1608 rebase on package_python_3_4_lean
wolma
parents: 17
diff changeset
22 <package name="python3" version="3.4" />
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
23 </repository>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
24 </action>
13
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
25 <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action>
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
26 <!-- remove the plain python symlink from the venv to avoid its
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
27 accidental use by Galaxy, MiModD uses python3 explicitly -->
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
28 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
18
2742ad4d1608 rebase on package_python_3_4_lean
wolma
parents: 17
diff changeset
29
2742ad4d1608 rebase on package_python_3_4_lean
wolma
parents: 17
diff changeset
30 <!-- download and install setuptools (required to install rpy2) -->
20
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
31 <action type="change_directory">$TMP_WORK_DIR</action>
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
32 <action sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25" type="download_file">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action>
18
2742ad4d1608 rebase on package_python_3_4_lean
wolma
parents: 17
diff changeset
33 <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action>
2742ad4d1608 rebase on package_python_3_4_lean
wolma
parents: 17
diff changeset
34 <action type="change_directory">pypa-setuptools-1a981f2e5031</action>
19
8f108b41a149 Uploaded
wolma
parents: 18
diff changeset
35 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
18
2742ad4d1608 rebase on package_python_3_4_lean
wolma
parents: 17
diff changeset
36
2742ad4d1608 rebase on package_python_3_4_lean
wolma
parents: 17
diff changeset
37 <!-- download and install six (required by rpy2) -->
20
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
38 <action type="change_directory">$TMP_WORK_DIR</action>
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
39 <action sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5" type="download_file">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action>
18
2742ad4d1608 rebase on package_python_3_4_lean
wolma
parents: 17
diff changeset
40 <action type="shell_command">tar -xzf six_1.9.0_src_all.tar.gz</action>
2742ad4d1608 rebase on package_python_3_4_lean
wolma
parents: 17
diff changeset
41 <action type="change_directory">six-1.9.0</action>
19
8f108b41a149 Uploaded
wolma
parents: 18
diff changeset
42 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
18
2742ad4d1608 rebase on package_python_3_4_lean
wolma
parents: 17
diff changeset
43
13
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
44 <!-- download and install rpy2 -->
20
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
45 <action type="change_directory">$TMP_WORK_DIR</action>
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
46 <action sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441" type="download_file">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action>
17
b658c34ee3fd Uploaded
wolma
parents: 16
diff changeset
47 <action type="shell_command">tar -xzf rpy2_2.7.5_src_all.tar.gz</action>
b658c34ee3fd Uploaded
wolma
parents: 16
diff changeset
48 <action type="change_directory">rpy2-2.7.5</action>
13
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
49 <action type="set_environment_for_install">
15
92bd325c70da Uploaded
wolma
parents: 14
diff changeset
50 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
16
e676aa6997cc Uploaded
wolma
parents: 15
diff changeset
51 <package name="readline" version="6.3" />
13
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
52 </repository>
21
c46406466625 Uploaded
wolma
parents: 20
diff changeset
53 <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
13
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
54 <package name="R" version="3.2.1" />
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
55 </repository>
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
56 </action>
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
57 <action type="shell_command">
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
58 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp;
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
59 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp;
19
8f108b41a149 Uploaded
wolma
parents: 18
diff changeset
60 $INSTALL_DIR/MiModD_venv/bin/python3 setup.py install
13
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
61 </action>
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
62
f0b3871cb869 Uploaded
wolma
parents: 10
diff changeset
63 <!-- download and install MiModD -->
20
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
64 <action type="change_directory">$TMP_WORK_DIR</action>
17
b658c34ee3fd Uploaded
wolma
parents: 16
diff changeset
65 <action type="download_file">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action>
b658c34ee3fd Uploaded
wolma
parents: 16
diff changeset
66 <action type="shell_command">tar -xzf MiModD-0.1.7.2.tar.gz</action>
b658c34ee3fd Uploaded
wolma
parents: 16
diff changeset
67 <action type="change_directory">MiModD-0.1.7.2</action>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
68 <action type="set_environment_for_install">
16
e676aa6997cc Uploaded
wolma
parents: 15
diff changeset
69 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
70 <package name="zlib" version="1.2.8" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
71 </repository>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
72 </action>
20
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
73 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
19
8f108b41a149 Uploaded
wolma
parents: 18
diff changeset
74 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
20
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
75 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
19
8f108b41a149 Uploaded
wolma
parents: 18
diff changeset
76 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action>
20
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
77
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
78 <!-- configure environment -->
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
79 <action type="set_environment">
21
c46406466625 Uploaded
wolma
parents: 20
diff changeset
80 <!-- to make MiModD accessible it is sufficient to simply add the
c46406466625 Uploaded
wolma
parents: 20
diff changeset
81 venvs site-packages directory to PYTHONPATH;
c46406466625 Uploaded
wolma
parents: 20
diff changeset
82 SITE_PACKAGES_RELPATH will be made available by the python3
c46406466625 Uploaded
wolma
parents: 20
diff changeset
83 package, which all MiModD toolwrappers require -->
c46406466625 Uploaded
wolma
parents: 20
diff changeset
84 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/MiModD_venv/$SITE_PACKAGES_RELPATH</environment_variable>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
85 </action>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
86 </actions>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
87 </install>
20
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
88
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
89 <readme>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
90 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
91 Home-page: http://sourceforge.net/projects/mimodd/
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
92 Author: Wolfgang Maier
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
93 Author-email: wolfgang.maier@biologie.uni-freiburg.de
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
94 License: GPL
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
95 Download-URL: http://sourceforge.net/projects/mimodd/
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
96
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
97 MiModD - Identify Mutations from Whole-Genome Sequencing Data
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
98 *************************************************************
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
99
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
100 MiModD is an integrated solution for efficient and user-friendly analysis of
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
101 whole-genome sequencing (WGS) data from laboratory model organisms.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
102 It enables geneticists to identify the genetic mutations present in an organism
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
103 starting from just raw WGS read data and a reference genome without the help of
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
104 a trained bioinformatician.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
105
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
106 MiModD is designed for good performance on standard hardware and enables WGS
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
107 data analysis for most model organisms on regular desktop PCs.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
108
20
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
109 Detailed documentation of the software can be found at:
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
110
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
111 http://mimodd.readthedocs.io
aba6d9b1c1f1 Uploaded
wolma
parents: 19
diff changeset
112
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
113 </readme>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
114 </package>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
115 </tool_dependency>