Mercurial > repos > fubar > weblogo3

changeset 17:baa6a37ed578 draft

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Uploaded
author fubar
date Mon, 18 Nov 2013 02:21:55 -0500
parents 21bcfe99f623
children 91fa0a8ce39d
files rgweblogo/tool_dependencies.xml
diffstat 1 files changed, 43 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgweblogo/tool_dependencies.xml	Mon Nov 18 02:21:55 2013 -0500
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="numpy" version="1.7.1">
+        <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="blankenberg" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ghostscript" version="9.07">
+        <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="package_weblogo" version="3.3">
+        <install version="1.0">
+            <actions>
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="download_by_url">http://weblogo.googlecode.com/files/weblogo-3.3.tar.gz</action>
+                <action type="shell_command">echo `ls -lt` &amp;&amp; echo `pwd`</action>
+                
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="c842299349c0" name="package_ghostscript_9_07" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                        <package name="ghostscript" version="9.07" />
+                    </repository>
+                    <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                        <package name="numpy" version="1.7.1" />
+                    </repository>
+                </action>
+                <!-- install weblogo -->
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY:$PYTHONPATH &amp;&amp; 
+                    python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="PYTHONPATH">$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="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="WEBLOGO_PATH">$INSTALL_DIR/bin/weblogo</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            weblogo3 is a python version of the old weblogo2.8 or so. Requires numpy and ghostscript so these are installed if not already on your system - if that happens, please be patient
+            while numpy compiles - especially if the ATLAS libraries are being installed - which is not at present.
+        </readme>
+     </package>
+</tool_dependency>