Mercurial > repos > nml > package_python_3_4_biopython_1_66

changeset 0:cb43753d0467 draft default tip

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_biopython_1_66 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
author nml
date Thu, 07 Jul 2016 09:56:45 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 39 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 07 09:56:45 2016 -0400
@@ -0,0 +1,39 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="python" version="3.4">
+        <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.10.1">
+        <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="biopython" version="1.66">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://biopython.org/DIST/biopython-1.66.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.10.1" />
+                    </repository>
+                    <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="python" version="3.4" />
+                    </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;
+                    python3 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>