Mercurial > repos > nml > package_python_3_4_bioext_0_17_3

comparison tool_dependencies.xml @ 0:d71e21675123 draft

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
author nml
date Thu, 07 Jul 2016 09:57:47 -0400
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children 1ca9f5fd8b65
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-1:000000000000 0:d71e21675123
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="python" version="3.4">
4 <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="pysam" version="0.8.3">
7 <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="numpy" version="1.10.1">
10 <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="biopython" version="1.66">
13 <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="bioext" version="0.17.3">
16 <install version="1.0">
17 <actions>
18 <action type="download_by_url">https://github.com/veg/BioExt/archive/0.17.3.tar.gz</action>
19 <action type="set_environment_for_install">
20 <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
21 <package name="pysam" version="0.8.3" />
22 </repository>
23 <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
24 <package name="numpy" version="1.10.1" />
25 </repository>
26 <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
27 <package name="biopython" version="1.66" />
28 </repository>
29 <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
30 <package name="python" version="3.4" />
31 </repository>
32 </action>
33 <action type="make_directory">$INSTALL_DIR/lib/python</action>
34 <action type="shell_command">
35 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
36 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
37 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
38 python3 setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
39 </action>
40 <action type="set_environment">
41 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
42 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
43 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable>
44 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
45 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOPYTHON]</environment_variable>
46 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
47 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
48 <environment_variable action="set_to" name="PYTHONPATH_BIOEXT">$INSTALL_DIR/lib/python</environment_variable>
49 <environment_variable action="set_to" name="PATH_BIOEXT">$INSTALL_DIR/bin</environment_variable>
50 </action>
51 </actions>
52 </install>
53 <readme>A few handy bioinformatics tools not already within BioPython</readme>
54 </package>
55 </tool_dependency>