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comparison tool_dependencies.xml @ 2:d2283cca00cd draft

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CEAS tool version 1.0.2-3: updates to get R 3.1.2 and bx-python 0.7.1 dependencies from the toolshed.
author pjbriggs
date Tue, 18 Oct 2016 09:31:10 -0400
parents f411ce97a351
children
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1:df9033b88b53 2:d2283cca00cd
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <!-- Local version of R 3.1.2 dependency --> 3 <!-- R 3.1.2 from main/test toolshed -->
4 <package name="R" version="3.1.2"> 4 <package name="R" version="3.1.2">
5 <install version="1.0"> 5 <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
6 <actions> 6 </package>
7 <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.2.tar.gz</action> 7 <!-- bx_python from main/test toolshed -->
8 <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> 8 <package name="bx-python" version="0.7.1">
9 <action type="make_install" /> 9 <repository changeset_revision="7ce9cf37130f" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
10 <action type="set_environment">
11 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
12 </action>
13 </actions>
14 </install>
15 </package> 10 </package>
16 <!-- Python mysqldb package --> 11 <!-- Python mysqldb package -->
17 <package name="python_mysqldb" version="1.2.5"> 12 <package name="python_mysqldb" version="1.2.5">
18 <install version="1.0"> 13 <install version="1.0">
19 <actions> 14 <actions>
28 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
29 </action> 24 </action>
30 </actions> 25 </actions>
31 </install> 26 </install>
32 <readme>Installs Python module MySQLdb 1.2.5</readme> 27 <readme>Installs Python module MySQLdb 1.2.5</readme>
33 </package>
34 <!-- bx_python
35 This is cribbed from devteam's 'package_bx_python_0_7' in the main
36 toolshed:
37 https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
38 -->
39 <package name="bx_python" version="0.7.1">
40 <install version="1.0">
41 <actions>
42 <action type="setup_virtualenv">
43 numpy==1.7.1
44 bx-python==0.7.1
45 </action>
46 <action type="set_environment">
47 <environment_variable action="set_to" name="BX_PYTHON_PATH">$INSTALL_DIR</environment_variable>
48 </action>
49 </actions>
50 </install>
51 <readme>
52 Installation of bx-python 0.7.1 along with numpy 1.7.1. The installation can be
53 accessed via BX_PYTHON_PATH.
54 </readme>
55 </package> 28 </package>
56 <!-- cistrome_ceas 29 <!-- cistrome_ceas
57 Installs the version of CEAS package found in the Cistrome 30 Installs the version of CEAS package found in the Cistrome
58 distribution: 31 distribution:
59 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview 32 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview