Mercurial > repos > iuc > package_biopython_1_61

changeset 0:5c57f6706664 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_biopython_1_61 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author iuc
date Tue, 19 May 2015 14:57:22 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 35 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 19 14:57:22 2015 -0400
@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="numpy" version="1.7.1">
+        <repository changeset_revision="c7ae57300a77" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </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="c7ae57300a77" name="package_numpy_1_7" owner="iuc" toolshed="https://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:$PYTHONPATH_NUMPY:$PYTHONPATH_MATPLOTLIB &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>
+            </actions>
+        </install>
+        <readme>The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.</readme>
+    </package>
+</tool_dependency>