Mercurial > repos > yhoogstrate > package_crossmap_0_2

comparison tool_dependencies.xml @ 1:803db5577b07 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
author yhoogstrate
date Fri, 28 Aug 2015 03:43:49 -0400
parents 805c8fbd3b4e
children e4de7f1284ce
comparison
equal deleted inserted replaced
0:805c8fbd3b4e 1:803db5577b07
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
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" />
5 </package>
6
3 <package name="numpy" version="1.9"> 7 <package name="numpy" version="1.9">
4 <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="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 9 </package>
6 10
7 <package name="cython" version="0.20.1"> 11 <package name="cython" version="0.23.1">
8 <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_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" />
9 </package> 13 </package>
10 14
11 <package name="crossmap" version="0.2"> 15 <package name="crossmap" version="0.2">
12 <install version="1.0"> 16 <install version="1.0">
13 <actions> 17 <actions>
14 <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>
15 19
16 <action type="setup_python_environment"> 20 <action type="setup_python_environment">
17 <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 21 <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu">
18 <package name="cython" version="0.20.1" /> 22 <package name="nose" version="1.3.7" />
23 </repository>
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" />
19 </repository> 26 </repository>
20 <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 27 <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
21 <package name="numpy" version="1.9" /> 28 <package name="numpy" version="1.9" />
22 </repository> 29 </repository>
23 </action> 30 </action>
26 Therefore install it with a manual shell_command instead 33 Therefore install it with a manual shell_command instead
27 of <package></package> inside a pyton_env. --> 34 of <package></package> inside a pyton_env. -->
28 <action type="shell_command"> 35 <action type="shell_command">
29 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "bin/CrossMap.py" ; 36 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "bin/CrossMap.py" ;
30 37
38 export PYTHONPATH="$CYTHON_PATH/lib:$PYTHONPATH" &amp;&amp;
39 export PYTHONPATH="$CYTHON_PATH/lib/python:$PYTHONPATH" &amp;&amp;
31 export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp; 40 export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp;
32 41
33 python setup.py install --root $INSTALL_DIR 42 python setup.py install --root $INSTALL_DIR
34 </action> 43 </action>
35 44