Mercurial > repos > yhoogstrate > package_crossmap_0_2

comparison tool_dependencies.xml @ 12:92ac3fa57a7e draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095-dirty
author yhoogstrate
date Fri, 28 Aug 2015 07:44:44 -0400
parents 8bff97f30fde
children b12b628ee597
comparison
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11:8bff97f30fde 12:92ac3fa57a7e
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <!--<package name="python" version="2.7">
4 <repository name="package_python_2_7" owner="iuc" prior_installation_required="True" />
5 </package>-->
6
7 <package name="nose" version="1.3.7"> 3 <package name="nose" version="1.3.7">
8 <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
9 </package> 5 </package>
10 6
11 <package name="numpy" version="1.9"> 7 <package name="numpy" version="1.9">
12 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 8 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
13 </package> 9 </package>
14 10
15 <package name="cython" version="0.23.1"> 11 <package name="cython" version="0.23.1">
16 <repository changeset_revision="226a91b737f9" name="package_cython_0_23_1" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 12 <repository changeset_revision="1c30e09f01a5" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
17 </package> 13 </package>
18 14
19 <package name="crossmap" version="0.2"> 15 <package name="crossmap" version="0.2">
20 <install version="1.0"> 16 <install version="1.0">
21 <actions> 17 <actions>
22 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action> 18 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action>
23 19
24 <action type="setup_python_environment"> 20 <action type="setup_python_environment">
25 <!--
26 <repository name="package_python_2_7" owner="iuc">
27 <package name="python" version="2.7" />
28 </repository>
29 -->
30 <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu"> 21 <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu">
31 <package name="nose" version="1.3.7" /> 22 <package name="nose" version="1.3.7" />
32 </repository> 23 </repository>
33 <repository changeset_revision="226a91b737f9" name="package_cython_0_23_1" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu"> 24 <repository changeset_revision="1c30e09f01a5" name="package_cython_0_23_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
34 <package name="cython" version="0.23.1" /> 25 <package name="cython" version="0.23.1" />
35 </repository> 26 </repository>
36 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 27 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
37 <package name="numpy" version="1.9" /> 28 <package name="numpy" version="1.9" />
38 </repository> 29 </repository>
39 </action> 30 </action>
40 31
41 <!-- CrossMap doesn't pick up the correct Cython path. 32 <!-- If CrossMap is installed with - - home or - - prefix
42 Therefore install it with a manual shell_command instead 33 into, it often crashes with a 'write-test' error
43 of <package></package> inside a pyton_env. --> 34
35 Using - - root places the installation in:
36 $INSTALL_DIR / (python path dir) /
37 -->
44 <action type="shell_command"> 38 <action type="shell_command">
45 which python ; 39 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ;
46 40
47 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "bin/CrossMap.py" ; 41 <!--
48
49 export PYTHONPATH="$CYTHON_PATH/lib:$PYTHONPATH" &amp;&amp; 42 export PYTHONPATH="$CYTHON_PATH/lib:$PYTHONPATH" &amp;&amp;
50 export PYTHONPATH="$CYTHON_PATH/lib/python:$PYTHONPATH" &amp;&amp; 43 export PYTHONPATH="$CYTHON_PATH/lib/python:$PYTHONPATH" &amp;&amp;
51 export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp; 44 export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp;
45 -->
52 46
53 echo $PYTHONPATH ; 47 python setup.py install --root $INSTALL_DIR &amp;&amp;
54 48 mv $INSTALL_DIR$(which python)/bin $INSTALL_DIR/bin &amp;&amp;
55 python setup.py install --root $INSTALL_DIR 49 mv $INSTALL_DIR$(which python)/lib $INSTALL_DIR/lib
56 </action> 50 </action>
57 51
58 <action type="set_environment"> 52 <action type="set_environment">
59 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable> 53 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
60 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/dist-packages</environment_variable> 54 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python"</environment_variable>
61 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable> 55 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
62 56
63 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable> 57 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable>
64 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable> 58 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
65 </action> 59 </action>