Mercurial > repos > lparsons > htseq_count

comparison tool_dependencies.xml @ 20:3b3601a2a7c7 draft

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
author lparsons
date Mon, 22 Jun 2015 17:01:05 -0400
parents d5edaf8dc974
children a6dcb86af112
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19:6f920f33c5eb 20:3b3601a2a7c7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 3
4 <package name="numpy" version="1.7.1">
5 <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
6 </package>
7
8 <package name="samtools" version="0.1.19"> 4 <package name="samtools" version="0.1.19">
9 <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> 5 <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
10 </package> 6 </package>
11 7
12 <package name="pysam" version="0.7.7"> 8 <package name="pysam" version="0.7.7">
13 <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 9 <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package> 10 </package>
15 11
16 <package name="htseq" version="0.6.1"> 12 <package name="htseq" version="0.6.1">
17 <install version="1.0"> 13 <repository changeset_revision="5b3da3e3543d" name="package_htseq_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
18 <actions>
19 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz</action>
20 <!-- populate the environment variables from the dependend repos -->
21 <action type="set_environment_for_install">
22 <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
23 <package name="numpy" version="1.7.1" />
24 </repository>
25 </action>
26 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
27 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
28 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
29 <action type="set_environment">
30 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
31 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
32 </action>
33 </actions>
34 </install>
35 <readme>
36 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
37 </readme>
38 </package> 14 </package>
39 15
40 </tool_dependency> 16 </tool_dependency>