Mercurial > repos > lparsons > htseq_count
comparison tool_dependencies.xml @ 20:3b3601a2a7c7 draft
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
author | lparsons |
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date | Mon, 22 Jun 2015 17:01:05 -0400 |
parents | d5edaf8dc974 |
children | a6dcb86af112 |
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19:6f920f33c5eb | 20:3b3601a2a7c7 |
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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 && 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> |