Mercurial > repos > bgruening > package_biopython_1_61

changeset 0:e87f0c6897a8 draft default tip

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author bgruening
date Fri, 07 Jun 2013 06:05:27 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 46 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Jun 07 06:05:27 2013 -0400
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+<?xml version="1.0"?>
+<tool_dependency>
+        <package name="numpy" version="1.7.1">
+            <repository changeset_revision="ad6ebe2c75ef" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="matplotlib" version="1.2.1">
+            <repository changeset_revision="c888aa8ed318" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        </package>
+        <!-- TODO reportlab -> Python Imaging Library
+        <package name="reportlab" version="1.2.1">
+            <repository name="package_reportlab_1_2" owner="bgruening" prior_installation_required="True" />
+        </package>
+        -->
+        <package name="biopython" version="1.61">
+            <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="c888aa8ed318" name="package_matplotlib_1_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <package name="matplotlib" version="1.2.1" />
+                        </repository>
+                        <repository changeset_revision="ad6ebe2c75ef" name="package_numpy_1_7" owner="bgruening" toolshed="http://testtoolshed.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:$PYTHONPATH_NUMPY:$PYTHONPATH_MATPLOTLIB &amp;&amp; 
+                    python setup.py install --home $INSTALL_DIR</action>
+                    <action type="set_environment">
+                        <environment_variable action="append_to" name="PYTHONPATH">$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>
+                </actions>
+            </install>
+            <readme>The PYTHONPATH for scipy can be accessed through PYTHONPATH_BIOPYTHON.</readme>
+        </package>
+</tool_dependency>