Mercurial > repos > yhoogstrate > package_crossmap_0_2

comparison tool_dependencies.xml @ 2:e4de7f1284ce draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
author yhoogstrate
date Wed, 04 Nov 2015 10:11:28 -0500
parents 803db5577b07
children bbc4d67d6a37
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1:803db5577b07 2:e4de7f1284ce
3 <package name="nose" version="1.3.7"> 3 <package name="nose" version="1.3.7">
4 <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 6
7 <package name="numpy" version="1.9"> 7 <package name="numpy" version="1.9">
8 <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 8 <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
9 </package> 9 </package>
10 10
11 <package name="cython" version="0.23.1"> 11 <package name="cython" version="0.23.1">
12 <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 12 <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
13 </package> 13 </package>
22 <package name="nose" version="1.3.7" /> 22 <package name="nose" version="1.3.7" />
23 </repository> 23 </repository>
24 <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 24 <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
25 <package name="cython" version="0.23.1" /> 25 <package name="cython" version="0.23.1" />
26 </repository> 26 </repository>
27 <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 27 <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
28 <package name="numpy" version="1.9" /> 28 <package name="numpy" version="1.9" />
29 </repository> 29 </repository>
30 </action> 30 </action>
31 31
32 <!-- CrossMap doesn't pick up the correct Cython path. 32 <!-- If CrossMap is installed with - - home or - - prefix
33 Therefore install it with a manual shell_command instead 33 into, it often crashes with a 'write-test' error
34 of <package></package> inside a pyton_env. --> 34
35 Using - - root places the installation in:
36 $INSTALL_DIR / (python path dir) /
37 -->
35 <action type="shell_command"> 38 <action type="shell_command">
36 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "bin/CrossMap.py" ; 39 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ;
37 40
38 export PYTHONPATH="$CYTHON_PATH/lib:$PYTHONPATH" &amp;&amp; 41 python setup.py install --root $INSTALL_DIR &amp;&amp;
39 export PYTHONPATH="$CYTHON_PATH/lib/python:$PYTHONPATH" &amp;&amp; 42 export SUB_DIR=$(dirname $(which python)) &amp;&amp;
40 export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp; 43 mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib &amp;&amp;
41 44 mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin
42 python setup.py install --root $INSTALL_DIR
43 </action> 45 </action>
44 46
45 <action type="set_environment"> 47 <action type="set_environment">
46 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable> 48 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python2.7/site-packages"</environment_variable>
47 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/dist-packages</environment_variable> 49 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
48 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
49 50
50 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable> 51 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable>
51 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable> 52 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
52 </action> 53 </action>
53 </actions> 54 </actions>
54 </install> 55 </install>
55 <readme> 56 <readme>