Mercurial > repos > lparsons > htseq_count
changeset 11:1a69449ae025
Setup numpy environment to install htseq
| author | lparsons |
|---|---|
| date | Tue, 05 Nov 2013 11:07:33 -0500 |
| parents | 7cc1db015f03 |
| children | c86659f03e98 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 7 insertions(+), 1 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Nov 04 16:50:35 2013 -0500 +++ b/tool_dependencies.xml Tue Nov 05 11:07:33 2013 -0500 @@ -2,7 +2,7 @@ <tool_dependency> <package name="numpy" version="1.7.1"> - <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.19"> @@ -17,6 +17,12 @@ <install version="1.0"> <actions> <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz</action> + <!-- populate the environment variables from the dependend repos --> + <action type="set_environment_for_install"> + <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="numpy" version="1.7.1" /> + </repository> + </action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>