Mercurial > repos > yhoogstrate > package_fuma_2_11_0

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
author yhoogstrate
date Fri, 20 Nov 2015 11:04:43 -0500
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-1:000000000000 0:f922f018f507
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="python" version="2.7">
4 <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6
7 <package name="htseq" version="0.6.1">
8 <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
9 </package>
10
11 <package name="fuma" version="2.11.0">
12 <install version="1.0">
13 <actions>
14 <action type="download_by_url">https://github.com/yhoogstrate/fuma/archive/4b3432078949523f93e523c501f6ed813ee23d35.tar.gz</action>
15
16 <action type="set_environment_for_install">
17 <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
18 <package name="python" version="2.7" />
19 </repository>
20
21 <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
22 <package name="htseq" version="0.6.1" />
23 </repository>
24 </action>
25
26 <action type="make_directory">$INSTALL_DIR/lib/python</action>
27 <action type="make_directory">$INSTALL_DIR/lib64/python</action>
28
29 <action type="shell_command">
30 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp;
31 python setup.py build &amp;&amp;
32 python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
33
34 ## Tests fails because the import of unittest goes wrong:
35 ## http://stackoverflow.com/questions/26893504/attributeerror-module-object-has-no-attribute-testcase
36 ## python setup.py test
37 </action>
38
39 <action type="set_environment">
40 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
41 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
42 </action>
43 </actions>
44 </install>
45 <readme>
46 Downloads and installs FuMa.
47
48 Prerequisites:
49 - git
50 </readme>
51 </package>
52 </tool_dependency>