Mercurial > repos > yating-l > jbrowse_hub

changeset 2:d048f9f9f9df draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Fri, 10 Mar 2017 14:27:54 -0500
parents 472f074fbf1f
children b01abbba3457
files jbrowse_hub.xml tool_dependencies.xml
diffstat 2 files changed, 40 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/jbrowse_hub.xml	Fri Mar 10 14:01:35 2017 -0500
+++ b/jbrowse_hub.xml	Fri Mar 10 14:27:54 2017 -0500
@@ -4,7 +4,8 @@
     </description>
 
     <requirements>
-        <requirement type="package" version="1.67">biopython_1_67</requirement>
+        <requirement type="package" version="1.9">numpy</requirement>
+        <requirement type="package" version="1.68">biopython</requirement>
     </requirements>
 
     <stdio>
--- a/tool_dependencies.xml	Fri Mar 10 14:01:35 2017 -0500
+++ b/tool_dependencies.xml	Fri Mar 10 14:27:54 2017 -0500
@@ -1,8 +1,43 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <!-- Biopython 1.67  -->
-    <package name="biopython_1_67" version="1.67">
-        <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="biopython" version="1.68">
+        <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">http://biopython.org/DIST/biopython-1.68.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="1e2b7e63dec2" name="package_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>