Mercurial > repos > iuc > package_pybedtools_0_6_6

comparison tool_dependencies.xml @ 0:cc2ed79fc537 draft

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author iuc
date Wed, 06 Aug 2014 17:52:14 -0400
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children 9084345ffde3
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-1:000000000000 0:cc2ed79fc537
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="tabix" version="0.2.6">
4 <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="samtools" version="0.1.19">
7 <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="bedtools" version="2.19.1">
10 <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="cython" version="0.20.1">
13 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="pybedtools" version="0.6.6">
16 <install version="1.0">
17 <actions>
18 <!-- first action is always downloading -->
19 <action type="download_by_url">https://github.com/daler/pybedtools/archive/v0.6.6.tar.gz</action>
20
21 <!-- populate the environment variables from the dependend repos -->
22 <action type="set_environment_for_install">
23 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
24 <package name="cython" version="0.20.1" />
25 </repository>
26 </action>
27
28 <action type="make_directory">$INSTALL_DIR/lib/python</action>
29 <action type="shell_command">
30 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
31 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
32 </action>
33
34 <action type="set_environment">
35 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
37 <environment_variable action="set_to" name="PYTHONPATH_PYBEDTOOLS">$INSTALL_DIR/lib/python</environment_variable>
38 <environment_variable action="set_to" name="PATH_PYBEDTOOLS">$INSTALL_DIR/bin</environment_variable>
39 <environment_variable action="set_to" name="PYBEDTOOLS_ROOT_DIR">$INSTALL_DIR</environment_variable>
40 </action>
41 </actions>
42 </install>
43 <readme>Compiling pybedtools requires cython and the gcc compiler.
44 https://github.com/daler/pybedtools
45 </readme>
46 </package>
47 </tool_dependency>