| Next changeset 1:f06c96348778 (2015-10-22) |
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Commit message:
Uploaded initial version, based on setup used for Biopython 1.61 |
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added:
tool_dependencies.xml |
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| diff -r 000000000000 -r 3e82cbc44886 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Sep 17 04:56:33 2013 -0400 |
| [ |
| @@ -0,0 +1,42 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="numpy" version="1.7.1"> + <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="biopython" version="1.62"> + <readme> +This Galaxy Tool Shed package installs Biopython from source, having +first installed NumPy which is a build time depencency. This requires +and assumes a standard C compiler is already installed, along with +the Python header files. + +Development of this dependency definition is being done here on GitHub: +https://github.com/biopython/galaxy_packages + +The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON. + </readme> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.62.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="numpy" version="1.7.1" /> + </repository> + </action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + export PATH=$PATH:$PATH_NUMPY && + export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY && + python setup.py install --install-lib $INSTALL_DIR/lib/python + </action> + <action type="set_environment"> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> + <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> + <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency> |