Mercurial > repos > yhoogstrate > package_fuma_2_10_0

comparison tool_dependencies.xml @ 0:48783f711368 draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
author yhoogstrate
date Fri, 09 Oct 2015 10:22:48 -0400
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-1:000000000000 0:48783f711368
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="python" version="2.7">
4 <repository changeset_revision="5caf592bb259" 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="2.10.0">
12 <install version="1.0">
13 <actions>
14 <action type="set_environment_for_install">
15 <repository changeset_revision="5caf592bb259" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
16 <package name="python" version="2.7" />
17 </repository>
18
19 <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
20 <package name="htseq" version="0.6.1" />
21 </repository>
22 </action>
23
24 <action type="make_directory">$INSTALL_DIR/lib/python</action>
25 <action type="make_directory">$INSTALL_DIR/lib64/python</action>
26
27 <action type="shell_command">
28 git clone https://github.com/yhoogstrate/fuma.git fuma &amp;&amp;
29 cd fuma &amp;&amp;
30 git reset --hard 8bead7a4d4ce8bdf4b6fd64df0c474b003768697 &amp;&amp;
31
32 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp;
33 python setup.py build &amp;&amp;
34 python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin &amp;&amp;
35 python setup.py test
36 </action>
37
38 <action type="set_environment">
39 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
41
42 <environment_variable action="set_to" name="FUMA_PATH">$INSTALL_DIR/bin</environment_variable>
43 <environment_variable action="set_to" name="FUMA_ROOT_PATH">$INSTALL_DIR</environment_variable>
44 </action>
45 </actions>
46 </install>
47 <readme>
48 Downloads and installs FuMa.
49
50 Prerequisites:
51 - git
52 </readme>
53 </package>
54 </tool_dependency>