| Previous changeset 0:5d5355863287 (2015-12-15) Next changeset 2:c722591ee0aa (2015-12-16) |
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Commit message:
Deleted selected files |
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removed:
tool_dependencies.xml |
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| diff -r 5d5355863287 -r 6f8b786e347b tool_dependencies.xml --- a/tool_dependencies.xml Tue Dec 15 11:08:33 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,45 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="python" version="2.7.10"> - <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="numpy" version="1.9"> - <repository changeset_revision="794f5cf3bb5d" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="biopython" version="1.66"> - <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-1.66.tar.gz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="794f5cf3bb5d" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="numpy" version="1.9" /> - </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> |