Mercurial > repos > biopython > package_biopython_1_63

changeset 0:a5c49b83e983 draft

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Uploaded initial version, based on setup used for Biopython 1.61 and 1.62
author biopython
date Tue, 18 Feb 2014 05:25:12 -0500
parents
children b2c685b0fbac
files tool_dependencies.xml
diffstat 1 files changed, 42 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Feb 18 05:25:12 2014 -0500
@@ -0,0 +1,42 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="numpy" version="1.7.1">
+        <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="biopython" version="1.63">
+        <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-1.63.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.7.1" />
+                    </repository>
+                </action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+                    export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
+                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &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="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
+                </action>
+            </actions>
+        </install>
+    </package>
+</tool_dependency>