Mercurial > repos > iuc > package_numpy_1_9

changeset 3:9cc1138e5e3e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_numpy_1_9 commit 26e1a6c62f83e82c02f2cdc10180090181ec0374-dirty
author iuc
date Fri, 02 Oct 2015 09:10:47 -0400
parents d6f39c80e75b
children c8f7a7d73466
files tool_dependencies.xml
diffstat 1 files changed, 30 insertions(+), 33 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Jul 17 10:41:25 2015 -0400
+++ b/tool_dependencies.xml	Fri Oct 02 09:10:47 2015 -0400
@@ -1,36 +1,33 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="atlas" version="3.10.2">
-        <repository changeset_revision="0538fd672119" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="python" version="2.7">
-        <repository changeset_revision="44bb4258922f" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.9">
-        <install version="1.0">
-            <actions>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="0538fd672119" name="package_atlas_3_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="atlas" version="3.10.2" />
-                    </repository>
-                </action>
-                <action type="setup_python_environment">
-                    <repository changeset_revision="44bb4258922f" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="python" version="2.7" />
-                    </repository>
-                    <!-- allow downloading and installing an Python package from https://pypi.org/ -->
-                    <package>https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz#md5#78842b73560ec378142665e712ae4ad9</package>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[ATLAS_LIB_DIR]</environment_variable>
-                    <environment_variable action="set_to" name="PYTHONPATH_NUMPY">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable action="set_to" name="PATH_NUMPY">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="set_to" name="NUMPY_ROOT_DIR">$INSTALL_DIR</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>
+        <package name="atlas" version="3.10.2">
+            <repository changeset_revision="0538fd672119" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="numpy" version="1.9">
+            <install version="1.0">
+                <actions>
+                    <action type="download_by_url">https://pypi.python.org/packages/source/n/numpy/numpy-1.9.0.tar.gz#md5#510cee1c6a131e0a9eb759aa2cc62609</action>
+                    <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                    <action type="set_environment_for_install">
+                        <repository changeset_revision="0538fd672119" name="package_atlas_3_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="atlas" version="3.10.2" />
+                        </repository>
+                    </action>
+                    <action type="shell_command">
+                        export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+                        export ATLAS=$ATLAS_ROOT_PATH &amp;&amp;
+                        python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
+                    </action>
+                    <action type="set_environment">
+                        <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                        <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                        <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[ATLAS_LIB_DIR]</environment_variable>
+                        <environment_variable action="set_to" name="PYTHONPATH_NUMPY">$INSTALL_DIR</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>