Mercurial > repos > iuc > package_numpy_1_7_with_atlas

changeset 0:23e6e24908eb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_numpy_1_7_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author iuc
date Tue, 19 May 2015 14:59:37 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 44 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 19 14:59:37 2015 -0400
@@ -0,0 +1,44 @@
+<?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">
+            <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="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>
+                    </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 $env.INSTALL_DIR/bin
+                    </action>
+                    <action type="set_environment">
+                        <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                        <environment_variable action="set_to" name="PYTHONPATH_NUMPY">$INSTALL_DIR/lib/python</environment_variable>
+                        <environment_variable action="set_to" name="PATH_NUMPY">$INSTALL_DIR/bin</environment_variable>
+                        </action>
+                </actions>
+            </install>
+            <readme>Compiling numpy requires a C and Fortran compiler (typically gcc and gfortran). The PYTHONPATH for numpy can be accessed through PYTHONPATH_NUMPY and the binaries with PATH_NUMPY.</readme>
+        </package>
+</tool_dependency>