Mercurial > repos > mzytnicki > s_mart

changeset 111:1409d4dbf17e draft

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Uploaded
author mzytnicki
date Wed, 24 Apr 2013 06:23:03 -0400
parents 040e446fcdc4
children c181ca344322
files tool_dependencies.xml
diffstat 1 files changed, 21 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Apr 24 06:04:10 2013 -0400
+++ b/tool_dependencies.xml	Wed Apr 24 06:23:03 2013 -0400
@@ -3,6 +3,27 @@
     <set_environment version="1.0">
         <environment_variable name="PYTHONPATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
+    <package name="samtools" version="0.1.12">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://github.com/modENCODE-DCC/Galaxy/blob/master/tool_shed_dependencies/bamedit/samtoolspkg.tar</action>
+                <action type="shell_command">chmod ago+x samtools</action>
+                <action type="shell_command">chmod ago+x maq2sam-long</action>
+                <action type="move_file">
+                    <source>samtools</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>maq2sam-long</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
+    </package>
 	<package name="R_PACKAGES">
 		<install version="1.0">
 			<actions>