Mercurial > repos > nml > package_python_3_4_bioext_0_17_3
changeset 0:d71e21675123 draft
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
| author | nml |
|---|---|
| date | Thu, 07 Jul 2016 09:57:47 -0400 |
| parents | |
| children | 1ca9f5fd8b65 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 55 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jul 07 09:57:47 2016 -0400 @@ -0,0 +1,55 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="python" version="3.4"> + <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="pysam" version="0.8.3"> + <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="numpy" version="1.10.1"> + <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="biopython" version="1.66"> + <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bioext" version="0.17.3"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://github.com/veg/BioExt/archive/0.17.3.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="pysam" version="0.8.3" /> + </repository> + <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="numpy" version="1.10.1" /> + </repository> + <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="biopython" version="1.66" /> + </repository> + <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="python" version="3.4" /> + </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 && + python3 setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> + <action type="set_environment"> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable> + <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> + <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOPYTHON]</environment_variable> + <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="PYTHONPATH_BIOEXT">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="set_to" name="PATH_BIOEXT">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>A few handy bioinformatics tools not already within BioPython</readme> + </package> +</tool_dependency>