Mercurial > repos > iuc > package_scikit_learn_0_13_with_atlas

changeset 0:6a4f25a9fbf4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scikit_learn_0_13_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author iuc
date Tue, 19 May 2015 15:02:07 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 73 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 19 15:02:07 2015 -0400
@@ -0,0 +1,73 @@
+<?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">
+            <repository changeset_revision="20d1dd0220d7" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="matplotlib" version="1.2.1">
+            <repository changeset_revision="a03ee94316b5" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        </package>
+
+        <package name="scikit_learn" version="0.13.1">
+            <install version="1.0">
+                <actions>
+                    <action type="download_by_url">https://pypi.python.org/packages/source/s/scikit-learn/scikit-learn-0.13.1.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>
+                        <repository changeset_revision="20d1dd0220d7" name="package_scipy_0_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="scipy" version="0.12.0" />
+                        </repository>
+                        <repository changeset_revision="a03ee94316b5" name="package_matplotlib_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="matplotlib" version="1.2.1" />
+                        </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 &amp;&amp;
+
+                    #if env.get('ATLAS_LIB_DIR', False):
+                        export ATLAS=$env.ATLAS_LIB_DIR/libatlas.a &amp;&amp;
+                    #end if
+                    #if env.get('LAPACK_LIB_DIR', False):
+                        export BLAS=$env.LAPACK_LIB_DIR/libblas.a &amp;&amp;
+                        export LAPACK=$env.LAPACK_LIB_DIR/liblapack.a &amp;&amp;
+                    #end if
+
+                    export PATH=\$PATH:$env.PATH_NUMPY &amp;&amp;
+                    export PYTHONPATH=\$PYTHONPATH:$env.PYTHONPATH_NUMPY:$env.PYTHONPATH_SCIPY:$env.PYTHONPATH_MATPLOTLIB &amp;&amp;
+
+                    python setup.py install --install-lib $env.INSTALL_DIR/lib/python
+                    </action>
+                    <action type="set_environment">
+                        <environment_variable action="append_to" name="PYTHONPATH">$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">$ENV[PATH_NUMPY]</environment_variable>
+                        <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
+                        <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
+
+                        <environment_variable action="set_to" name="PYTHONPATH_SCIKIT_LEARN">$INSTALL_DIR/lib/python</environment_variable>
+                        </action>
+                </actions>
+            </install>
+            <readme>Compiling scikit-learn requires a C compiler (typically gcc). The PYTHONPATH for scikit-learn can be accessed through PYTHONPATH_SCIKIT_LEARN.</readme>
+        </package>
+</tool_dependency>