Mercurial > repos > iuc > package_numpy_1_7

changeset 1:74c21f9bdc39 draft

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revert the cheetah template until the next stable Galaxy release it out. Fallback to non atlas/lapack numpy.
author bgruening
date Mon, 12 Aug 2013 10:00:18 -0400
parents c75482be1d3a
children 028df1ddd7a2
files tool_dependencies.xml
diffstat 1 files changed, 2 insertions(+), 26 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Sun Aug 11 06:44:19 2013 -0400
+++ b/tool_dependencies.xml	Mon Aug 12 10:00:18 2013 -0400
@@ -1,36 +1,12 @@
 <?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="http://toolshed.g2.bx.psu.edu" />
-        </package>
-        <package name="atlas" version="3.10.1">
-            <repository changeset_revision="597c0e54eded" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
-        </package>
         <package name="numpy" version="1.7.1">
             <install version="1.0">
                 <actions>
                     <action type="download_by_url">https://pypi.python.org/packages/source/n/numpy/numpy-1.7.1.tar.gz</action>
-                    <action type="set_environment_for_install">
-                        <repository changeset_revision="597c0e54eded" name="package_atlas_3_10" owner="iuc" toolshed="http://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="http://toolshed.g2.bx.psu.edu">
-                            <package name="lapack" version="3.4.2" />
-                        </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
-                    python setup.py install --install-lib $env.INSTALL_DIR/lib/python --install-scripts $env.INSTALL_DIR/bin
-                    </action>
+                    <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
+                    python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                     <action type="set_environment">
                         <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                         <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>