Mercurial > repos > biopython > package_biopython_1_65
annotate tool_dependencies.xml @ 1:b3a791f6e3ba draft default tip
planemo upload for repository https://github.com/biopython/galaxy_packages/tree/master/package_biopython_1_65 commit 985e29ac10e02dd97a3e155d881513658448e85a
| author | biopython |
|---|---|
| date | Thu, 22 Oct 2015 09:05:20 -0400 |
| parents | f8d72690eeae |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="numpy" version="1.9"> | |
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b3a791f6e3ba
planemo upload for repository https://github.com/biopython/galaxy_packages/tree/master/package_biopython_1_65 commit 985e29ac10e02dd97a3e155d881513658448e85a
biopython
parents:
0
diff
changeset
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4 <repository changeset_revision="816d3480b0b1" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 0 | 5 </package> |
| 6 <package name="biopython" version="1.65"> | |
| 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> | |
| 18 <install version="1.0"> | |
| 19 <actions> | |
| 20 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz</action> | |
| 21 <action type="set_environment_for_install"> | |
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1
b3a791f6e3ba
planemo upload for repository https://github.com/biopython/galaxy_packages/tree/master/package_biopython_1_65 commit 985e29ac10e02dd97a3e155d881513658448e85a
biopython
parents:
0
diff
changeset
|
22 <repository changeset_revision="816d3480b0b1" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 23 <package name="numpy" version="1.9" /> |
| 24 </repository> | |
| 25 </action> | |
| 26 <action type="make_directory">$INSTALL_DIR/lib/python</action> | |
| 27 <action type="shell_command"> | |
| 28 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && | |
| 29 export PATH=$PATH:$PATH_NUMPY && | |
| 30 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY && | |
| 31 python setup.py install --install-lib $INSTALL_DIR/lib/python | |
| 32 </action> | |
| 33 <action type="set_environment"> | |
| 34 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> | |
| 35 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> | |
| 36 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> | |
| 37 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable> | |
| 38 </action> | |
| 39 </actions> | |
| 40 </install> | |
| 41 </package> | |
| 42 </tool_dependency> |