Mercurial > repos > biopython > package_biopython_1_61

changeset 3:2f6c871cfa35 draft

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Remove last bit of MatPlotLib
author peterjc
date Tue, 17 Sep 2013 04:49:17 -0400
parents 54e5c64b0460
children 89f98445faf4
files tool_dependencies.xml
diffstat 1 files changed, 15 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Aug 19 17:09:02 2013 -0400
+++ b/tool_dependencies.xml	Tue Sep 17 04:49:17 2013 -0400
@@ -1,14 +1,25 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="793c48909d53" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="biopython" version="1.61">
+        <readme>
+This Galaxy Tool Shed package installs Biopython from source, having
+first installed NumPy which is a build time depencency. This requires
+and assumes a standard C compiler is already installed, along with
+the Python header files.
+
+Development of this dependency definition is being done here on GitHub:
+https://github.com/biopython/galaxy_packages
+
+The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
+        </readme>
         <install version="1.0">
             <actions>
                 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action>
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="793c48909d53" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="numpy" version="1.7.1" />
                     </repository>
                 </action>
@@ -16,20 +27,16 @@
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                     export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
-                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY:$PYTHONPATH_MATPLOTLIB &amp;&amp; 
+                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp; 
                     python setup.py install --install-lib $INSTALL_DIR/lib/python
                 </action>
                 <action type="set_environment">
                     <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-
                     <environment_variable action="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">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
-
                     <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
-                    </action>
+                </action>
             </actions>
         </install>
-        <readme>The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.</readme>
     </package>
 </tool_dependency>