Mercurial > repos > ulfschaefer > package_python_2_7_biopython_1_66

changeset 0:81243480cf23 draft default tip

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author ulfschaefer
date Tue, 19 Apr 2016 09:33:08 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 50 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Apr 19 09:33:08 2016 -0400
@@ -0,0 +1,50 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="python" version="2.7.10">
+        <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+	<package name="numpy" version="1.9">
+        <repository changeset_revision="fe0870696ca7" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="biopython" version="1.66">
+        <readme>
+This package is a modified version of the package package_biopython_1_66
+owned by 'biopython' (copyright Peter Cock) revision 8433ee4531ff.
+Dependencies of this package have been modified to provide Biopython
+for Python 2.7.10.
+
+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-1.66.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="fe0870696ca7" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.9" />
+                    </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>