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Patch minimus2 during install (bug reported in 2011 not yet fixed in amos source)
author Jim Johnson <jj@umn.edu>
date Fri, 19 Jul 2013 08:01:23 -0500
parents 8ed847ebac73
children
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0:8ed847ebac73 1:b5e98e4efb18
8 </package> 8 </package>
9 <package name="amos" version="3.1.0"> 9 <package name="amos" version="3.1.0">
10 <install version="1.0"> 10 <install version="1.0">
11 <actions> 11 <actions>
12 <action type="download_by_url">http://sourceforge.net/projects/amos/files/amos/3.1.0/amos-3.1.0.tar.gz</action> 12 <action type="download_by_url">http://sourceforge.net/projects/amos/files/amos/3.1.0/amos-3.1.0.tar.gz</action>
13 <!-- patch this, since it has been a bug since 2011 -->
14 <action type="shell_command">sed -i.bak 's/dumpreads \(\$[(]BANK[)]\) \(-[mM]\) \(\$[(]REFCOUNT[)]\)/dumpreads \2 \3 \1/' src/Pipeline/minimus2.acf</action>
13 <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> 15 <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
14 <action type="shell_command">make</action> 16 <action type="shell_command">make</action>
15 <action type="shell_command">make install</action> 17 <action type="shell_command">make install</action>
16 <action type="set_environment"> 18 <action type="set_environment">
17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 19 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>