Mercurial > repos > modencode-dcc > macs2

changeset 0:3c1f5b892b2b draft

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Uploaded
author modencode-dcc
date Wed, 23 Jan 2013 13:38:38 -0500
parents
children 9aa25104162e
files tool_dependencies.xml
diffstat 1 files changed, 36 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Jan 23 13:38:38 2013 -0500
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <!--<set_environment version="1.0">
+        <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>-->
+    <package name="macs2" version="2.0.10.2">
+        <install version="1.0">           
+            <actions>
+                <action type="download_by_url">http://www.python.org/ftp/python/2.7.3/Python-2.7.3.tar.bz2</action>
+                <action type="shell_command">tar -xvf Python-2.7.3.tar.bz2</action>
+                <action type="shell_command">cd Python-2.7.3</action>
+                <action type="shell_command">./configure</action>
+                <action type="shell_command">make -j</action>
+                <action type="shell_command">sudo make install</action>
+                <action type="shell_command">sudo chmod ag+w /usr/local/lib/python2.7/site-packages</action>
+                <action type="shell_command">sudo chmod ag+wx /usr/local/bin</action>
+            </actions>
+            <actions>
+                <action type="download_by_url">https://github.com/modENCODE-DCC/Galaxy/blob/master/toolshed/dependencies/macs2/macs2pkg.tar?raw=true</action>
+                <action type="move_directory_files">
+                    <source_directory>bin</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>lib</source_directory>
+                    <destination_directory>$INSTALL_DIR/lib</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Macs2 depends on having python2.7 installed on all nodes of the work cluster</readme>
+    </package>
+</tool_dependency>