Mercurial > repos > lparsons > htseq_count
annotate tool_dependencies.xml @ 13:30bb8acb77a4
Updated to v0.5.4p5, use repository dependencies.
author | lparsons |
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date | Tue, 05 Nov 2013 13:02:43 -0500 |
parents | 62a1de8c8aae |
children | 265ca0f35789 |
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1 <?xml version="1.0"?> |
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2 <tool_dependency> |
13 | 3 |
4 <package name="numpy" version="1.7.1"> | |
5 <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> | |
6 </package> | |
7 | |
8 <package name="samtools" version="0.1.19"> | |
9 <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> | |
10 </package> | |
11 | |
12 <package name="picard" version="1.56.0"> | |
13 <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> | |
14 </package> | |
15 | |
16 <package name="htseq" version="0.5.4p5"> | |
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17 <install version="1.0"> |
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18 <actions> |
13 | 19 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz</action> |
20 <!-- populate the environment variables from the dependend repos --> | |
21 <action type="set_environment_for_install"> | |
22 <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> | |
23 <package name="numpy" version="1.7.1" /> | |
24 </repository> | |
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25 </action> |
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62a1de8c8aae
Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist
lparsons
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26 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> |
62a1de8c8aae
Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist
lparsons
parents:
10
diff
changeset
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27 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> |
62a1de8c8aae
Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist
lparsons
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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 $INSTALL_DIR/bin</action> |
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29 <action type="set_environment"> |
13 | 30 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> |
31 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
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32 </action> |
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33 </actions> |
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34 </install> |
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35 <readme> |
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36 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package. |
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37 </readme> |
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38 </package> |
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39 |
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40 </tool_dependency> |