Mercurial > repos > yhoogstrate > package_crossmap_0_2
diff tool_dependencies.xml @ 2:e4de7f1284ce draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
| author | yhoogstrate |
|---|---|
| date | Wed, 04 Nov 2015 10:11:28 -0500 |
| parents | 803db5577b07 |
| children | bbc4d67d6a37 |
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--- a/tool_dependencies.xml Fri Aug 28 03:43:49 2015 -0400 +++ b/tool_dependencies.xml Wed Nov 04 10:11:28 2015 -0500 @@ -5,7 +5,7 @@ </package> <package name="numpy" version="1.9"> - <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="cython" version="0.23.1"> @@ -24,30 +24,31 @@ <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="cython" version="0.23.1" /> </repository> - <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="numpy" version="1.9" /> </repository> </action> - <!-- CrossMap doesn't pick up the correct Cython path. - Therefore install it with a manual shell_command instead - of <package></package> inside a pyton_env. --> + <!-- If CrossMap is installed with - - home or - - prefix + into, it often crashes with a 'write-test' error + + Using - - root places the installation in: + $INSTALL_DIR / (python path dir) / + --> <action type="shell_command"> - sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "bin/CrossMap.py" ; + sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ; - export PYTHONPATH="$CYTHON_PATH/lib:$PYTHONPATH" && - export PYTHONPATH="$CYTHON_PATH/lib/python:$PYTHONPATH" && - export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" && - - python setup.py install --root $INSTALL_DIR + python setup.py install --root $INSTALL_DIR && + export SUB_DIR=$(dirname $(which python)) && + mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib && + mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin </action> <action type="set_environment"> - <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable> - <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/dist-packages</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python2.7/site-packages"</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable> + <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable> <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable> </action> </actions>