Mercurial > repos > pjbriggs > ceas

annotate tool_dependencies.xml @ 9:4c3b7130dbbb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Bump version to 1.0.2-3 to reflect dependency updates.
author pjbriggs
date Tue, 18 Oct 2016 09:24:30 -0400
parents c9c4792d0876
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
1 <?xml version="1.0"?>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
2 <tool_dependency>
6
55ed5e1b7a07 Get R 3.1.2 dependency from toolshed.
pjbriggs
parents: 4
diff changeset
3 <!-- R 3.1.2 from main/test toolshed -->
2
695d61decd06 Make dependency on R explicit.
pjbriggs
parents: 0
diff changeset
4 <package name="R" version="3.1.2">
6
55ed5e1b7a07 Get R 3.1.2 dependency from toolshed.
pjbriggs
parents: 4
diff changeset
5 <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
2
695d61decd06 Make dependency on R explicit.
pjbriggs
parents: 0
diff changeset
6 </package>
7
7ed66f11cdcc Install bx_python dependency from toolshed.
pjbriggs
parents: 6
diff changeset
7 <!-- bx_python from main/test toolshed -->
8
c9c4792d0876 Fix requirement for bx-python dependency.
pjbriggs
parents: 7
diff changeset
8 <package name="bx-python" version="0.7.1">
7
7ed66f11cdcc Install bx_python dependency from toolshed.
pjbriggs
parents: 6
diff changeset
9 <repository changeset_revision="6a811020ff2f" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
7ed66f11cdcc Install bx_python dependency from toolshed.
pjbriggs
parents: 6
diff changeset
10 </package>
2
695d61decd06 Make dependency on R explicit.
pjbriggs
parents: 0
diff changeset
11 <!-- Python mysqldb package -->
0
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
12 <package name="python_mysqldb" version="1.2.5">
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
13 <install version="1.0">
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
14 <actions>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
15 <action type="download_by_url">https://pypi.python.org/packages/source/M/MySQL-python/MySQL-python-1.2.5.zip</action>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
16 <action type="make_directory">$INSTALL_DIR/lib/python</action>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
17 <action type="shell_command">
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
18 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
19 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
20 </action>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
21 <action type="set_environment">
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
22 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
24 </action>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
25 </actions>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
26 </install>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
27 <readme>Installs Python module MySQLdb 1.2.5</readme>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
28 </package>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
29 <!-- cistrome_ceas
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
30 Installs the version of CEAS package found in the Cistrome
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
31 distribution:
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
32 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
33 -->
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
34 <package name="cistrome_ceas" version="1.0.2.d8c0751">
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
35 <install version="1.0">
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
36 <actions>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
37 <action type="shell_command">
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
38 hg clone https://bitbucket.org/cistrome/cistrome-applications-harvard cistrome_ceas
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
39 </action>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
40 <action type="shell_command">
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
41 hg update d8c0751
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
42 </action>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
43 <action type="make_directory">$INSTALL_DIR/lib/python</action>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
44 <action type="shell_command">
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
45 cd published-packages/CEAS/
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
46 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
47 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
48 </action>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
49 <action type="set_environment">
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
50 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
51 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
52 </action>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
53 </actions>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
54 </install>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
55 <readme>Installs version 1.0.2 of CEAS from cistrome (commit id d8c0751,
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
56 datestamp 20140929), which includes ceasBW (a version of ceas which can
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
57 handle bigWig file input from MACS2.
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
58
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
59 Cistrome code is at
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
60 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
61
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
62 The CEAS code is under the published-packages/CEAS/ subdirectory
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
63
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
64 Cistrome data files and documentation can be found at
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
65 http://liulab.dfci.harvard.edu/CEAS/index.html
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
66 </readme>
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
67 </package>
4
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
68 <!-- fetchChromSize from UCSC tools -->
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
69 <package name="ucsc_fetchChromSizes" version="1.0">
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
70 <install version="1.0">
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
71 <actions>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
72 <action type="download_binary">
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
73 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
74 </action>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
75 <action type="chmod">
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
76 <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
77 </action>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
78 <action type="set_environment">
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
79 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
80 </action>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
81 </actions>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
82 </install>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
83 <readme>Installs the binary executable for the fetchChromSizes utility
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
84 from UCSC tools
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
85 </readme>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015)
pjbriggs
parents: 2
diff changeset
86 </package>
0
8b25779ee261 Uploaded initial version to test toolshed.
pjbriggs
parents:
diff changeset
87 </tool_dependency>