Mercurial > repos > iuc > package_scipy_0_12_with_atlas

annotate tool_dependencies.xml @ 0:4f0a5111d99c draft default tip

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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
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4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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1 <?xml version="1.0"?>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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2 <tool_dependency>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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3 <package name="lapack" version="3.4.2">
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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4 <repository changeset_revision="98a7d116c15f" name="package_lapack_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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5 </package>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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6 <package name="atlas" version="3.10.1">
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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7 <repository changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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8 </package>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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9 <package name="numpy" version="1.7.1">
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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10 <repository changeset_revision="c7ae57300a77" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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11 </package>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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12 <package name="scipy" version="0.12.0">
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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13 <install version="1.0">
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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14 <actions>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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15 <action type="download_by_url">http://downloads.sourceforge.net/project/scipy/scipy/0.12.0/scipy-0.12.0.tar.gz</action>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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16 <action type="set_environment_for_install">
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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17 <repository changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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18 <package name="atlas" version="3.10.1" />
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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19 </repository>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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20 <repository changeset_revision="98a7d116c15f" name="package_lapack_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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21 <package name="lapack" version="3.4.2" />
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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22 </repository>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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23 <repository changeset_revision="c7ae57300a77" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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24 <package name="numpy" version="1.7.1" />
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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25 </repository>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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26 </action>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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27 <action type="make_directory">$INSTALL_DIR/lib/python</action>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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28 <action language="cheetah" type="template_command">
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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29 export PYTHONPATH=\$PYTHONPATH:$env.INSTALL_DIR/lib/python &amp;&amp;
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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30
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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31 #if env.get('ATLAS_LIB_DIR', False):
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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32 export ATLAS=$env.ATLAS_LIB_DIR/libatlas.a &amp;&amp;
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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33 #end if
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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34 #if env.get('LAPACK_LIB_DIR', False):
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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35 export BLAS=$env.LAPACK_LIB_DIR/libblas.a &amp;&amp;
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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36 export LAPACK=$env.LAPACK_LIB_DIR/liblapack.a &amp;&amp;
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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37 #end if
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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38
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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39 export PATH=\$PATH:$env.PATH_NUMPY &amp;&amp;
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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40 export PYTHONPATH=\$PYTHONPATH:$env.PYTHONPATH_NUMPY &amp;&amp;
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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41 python setup.py install --install-lib $env.INSTALL_DIR/lib/python --install-scripts $env.INSTALL_DIR/bin
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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42 </action>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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43 <action type="set_environment">
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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44 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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45 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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46 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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47 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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48 <environment_variable action="set_to" name="PYTHONPATH_SCIPY">$INSTALL_DIR/lib/python</environment_variable>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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49 <environment_variable action="set_to" name="PATH_SCIPY">$INSTALL_DIR/bin</environment_variable>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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50 </action>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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51 </actions>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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52 </install>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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53 <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>
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54 </package>
4f0a5111d99c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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55 </tool_dependency>