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changeset 25:09e6427d3e6a draft

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Use repository dependency for samtools
author Jim Johnson <jj@umn.edu>
date Mon, 18 Feb 2013 11:01:18 -0600
parents 6460f2ba6a60
children bac82f25d42a
files tool_dependencies.xml
diffstat 1 files changed, 1 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Dec 28 14:15:14 2012 -0600
+++ b/tool_dependencies.xml	Mon Feb 18 11:01:18 2013 -0600
@@ -45,26 +45,6 @@
         </readme>
     </package>
     <package name="samtools" version="0.1.18">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
-                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>misc/maq2sam-long</source>
-                    <destination>$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>
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_samtools_0_1_18" owner="devteam" changeset_revision="a7936f4ea405" />
     </package>
 </tool_dependency>