# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1374238883 18000
# Node ID b5e98e4efb1881614c4b900cd379af7eb98415f8
# Parent  8ed847ebac73db00004505275ff99ce31249884d
Patch minimus2 during install (bug reported in 2011 not yet fixed in amos source)

diff -r 8ed847ebac73 -r b5e98e4efb18 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jul 17 17:31:18 2013 -0400
+++ b/tool_dependencies.xml	Fri Jul 19 08:01:23 2013 -0500
@@ -10,6 +10,8 @@
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://sourceforge.net/projects/amos/files/amos/3.1.0/amos-3.1.0.tar.gz</action>
+                <!-- patch this, since it has been a bug since 2011 -->
+                <action type="shell_command">sed -i.bak 's/dumpreads \(\$[(]BANK[)]\) \(-[mM]\) \(\$[(]REFCOUNT[)]\)/dumpreads \2 \3 \1/' src/Pipeline/minimus2.acf</action>
                 <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
                 <action type="shell_command">make</action>
                 <action type="shell_command">make install</action>