Mercurial > repos > iuc > package_scipy_0_12_with_atlas
changeset 0:4f0a5111d99c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
| author | iuc |
|---|---|
| date | Tue, 19 May 2015 15:02:23 -0400 |
| parents | |
| children | |
| 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 Tue May 19 15:02:23 2015 -0400 @@ -0,0 +1,55 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="lapack" version="3.4.2"> + <repository changeset_revision="98a7d116c15f" name="package_lapack_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="atlas" version="3.10.1"> + <repository changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="numpy" version="1.7.1"> + <repository changeset_revision="c7ae57300a77" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="scipy" version="0.12.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/scipy/scipy/0.12.0/scipy-0.12.0.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="atlas" version="3.10.1" /> + </repository> + <repository changeset_revision="98a7d116c15f" name="package_lapack_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="lapack" version="3.4.2" /> + </repository> + <repository changeset_revision="c7ae57300a77" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="numpy" version="1.7.1" /> + </repository> + </action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action language="cheetah" type="template_command"> + export PYTHONPATH=\$PYTHONPATH:$env.INSTALL_DIR/lib/python && + + #if env.get('ATLAS_LIB_DIR', False): + export ATLAS=$env.ATLAS_LIB_DIR/libatlas.a && + #end if + #if env.get('LAPACK_LIB_DIR', False): + export BLAS=$env.LAPACK_LIB_DIR/libblas.a && + export LAPACK=$env.LAPACK_LIB_DIR/liblapack.a && + #end if + + export PATH=\$PATH:$env.PATH_NUMPY && + export PYTHONPATH=\$PYTHONPATH:$env.PYTHONPATH_NUMPY && + python setup.py install --install-lib $env.INSTALL_DIR/lib/python --install-scripts $env.INSTALL_DIR/bin + </action> + <action type="set_environment"> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> + <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> + <environment_variable action="set_to" name="PYTHONPATH_SCIPY">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="set_to" name="PATH_SCIPY">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Compiling scipy requires a C and Fortran compiler (typically gcc and gfortran). The PYTHONPATH for scipy can be accessed through PYTHONPATH_SCIPY and the binaries with PATH_SCIPY.</readme> + </package> +</tool_dependency>