Mercurial > repos > biopython > package_biopython_1_61

comparison tool_dependencies.xml @ 3:ae9dda584395 draft

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Removed trace of MatPlotLib
author peterjc
date Tue, 17 Sep 2013 04:54:28 -0400
parents b482933a6de5
children 689e9fb41527
comparison
equal deleted inserted replaced
2:b482933a6de5 3:ae9dda584395
2 <tool_dependency> 2 <tool_dependency>
3 <package name="numpy" version="1.7.1"> 3 <package name="numpy" version="1.7.1">
4 <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="biopython" version="1.61"> 6 <package name="biopython" version="1.61">
7 <readme>
8 This Galaxy Tool Shed package installs Biopython from source, having
9 first installed NumPy which is a build time depencency. This requires
10 and assumes a standard C compiler is already installed, along with
11 the Python header files.
12
13 Development of this dependency definition is being done here on GitHub:
14 https://github.com/biopython/galaxy_packages
15
16 The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
17 </readme>
7 <install version="1.0"> 18 <install version="1.0">
8 <actions> 19 <actions>
9 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action> 20 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action>
10 <action type="set_environment_for_install"> 21 <action type="set_environment_for_install">
11 <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> 22 <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
14 </action> 25 </action>
15 <action type="make_directory">$INSTALL_DIR/lib/python</action> 26 <action type="make_directory">$INSTALL_DIR/lib/python</action>
16 <action type="shell_command"> 27 <action type="shell_command">
17 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 28 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
18 export PATH=$PATH:$PATH_NUMPY &amp;&amp; 29 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
19 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY:$PYTHONPATH_MATPLOTLIB &amp;&amp; 30 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
20 python setup.py install --install-lib $INSTALL_DIR/lib/python 31 python setup.py install --install-lib $INSTALL_DIR/lib/python
21 </action> 32 </action>
22 <action type="set_environment"> 33 <action type="set_environment">
23 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> 34 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
24
25 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> 35 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
26 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> 36 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
27 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
28
29 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable> 37 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
30 </action> 38 </action>
31 </actions> 39 </actions>
32 </install> 40 </install>
33 <readme>The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.</readme>
34 </package> 41 </package>
35 </tool_dependency> 42 </tool_dependency>