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tool_dependencies.xml |
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| diff -r 000000000000 -r fbe9f90728fc tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu May 29 20:35:40 2014 -0400 |
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| @@ -0,0 +1,36 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="numpy" version="1.8.1"> + <repository changeset_revision="36659940cecb" name="package_numpy_1_8" owner="qfab" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" /> + </package> + <package name="pycogent" version="1.5.2"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://sourceforge.net/projects/pycogent/files/PyCogent/1.5.2/PyCogent-1.5.2.tgz/download</action> + <action type="make_directory">$INSTALL_DIR/cogent</action> + <action type="set_environment_for_install"> + <repository changeset_revision="36659940cecb" name="package_numpy_1_8" owner="qfab" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" > + <package name="numpy" version="1.8.1" /> + </repository> + <action type="shell_command"> + python -c "import numpy; print numpy.version.version" && env >> /opt/galaxy/log.txt: + </action> + </action> + <action type="shell_command"> + python setup.py build_ext -if + </action> + <action type="move_directory_files"> + <source_directory>cogent</source_directory> + <destination_directory>$INSTALL_DIR/cogent/</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable> + <environment_variable action="set_to" name="PATH_PYCOGENT">$INSTALL_DIR</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> + <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> + </action> + </actions> + </install> + <readme>It is required to install a numpy python package (here numpy python package version 1.8.1) before installing the pycogent package.</readme> + </package> +</tool_dependency> |