|
43
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3 <package name="numpy" version="1.7">
|
|
|
4 <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
|
|
|
5 </package>
|
|
|
6 <package name="pysam" version="0.7.6">
|
|
|
7 <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
|
|
|
8 </package>
|
|
|
9 <package name="freetype" version="2.4">
|
|
|
10 <repository changeset_revision="fe5cfaf931ff" name="package_freetype_2_4" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
|
|
|
11 </package>
|
|
|
12 <package name="matplotlib" version="1.2">
|
|
|
13 <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
|
|
|
14 </package>
|
|
|
15 <package name="htseq" version="0.5.4p3">
|
|
|
16 <install version="1.0">
|
|
|
17 <actions>
|
|
44
|
18 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
|
|
|
19 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
|
|
43
|
20 <action type="set_environment_for_install">
|
|
|
21 <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
|
|
|
22 <package name="numpy" version="1.7" />
|
|
|
23 </repository>
|
|
|
24 <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
|
|
|
25 <package name="pysam" version="0.7.6" />
|
|
|
26 </repository>
|
|
|
27 <repository changeset_revision="fe5cfaf931ff" name="package_freetype_2_4" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
|
|
|
28 <package name="freetype" version="2.4" />
|
|
|
29 </repository>
|
|
|
30 <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
|
|
|
31 <package name="matplotlib" version="1.2" />
|
|
|
32 </repository>
|
|
|
33 </action>
|
|
|
34 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action>
|
|
|
35 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
|
|
|
36 <action type="set_environment">
|
|
|
37 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
|
|
|
38 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
|
|
|
39 </action>
|
|
|
40 </actions>
|
|
|
41 </install>
|
|
|
42 <readme>
|
|
|
43 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), pysam and the Numpy Python package.
|
|
|
44 Note this uses the matplotlib lite version dependent on the lite version of numpy - no atlas compilation
|
|
|
45 </readme>
|
|
|
46 </package>
|
|
|
47 </tool_dependency>
|
