# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1358106536 21600
# Node ID 57841f58676f50ddb29a3bf14aa3e5ef2227073f
# Parent  1ea6445491d48a9ed0e005f75c8d2c66e4cb82df
Add gmap_bin to defuse.xml configfile generation

diff -r 1ea6445491d4 -r 57841f58676f defuse.xml
--- a/defuse.xml	Mon Jan 07 14:52:26 2013 -0600
+++ b/defuse.xml	Sun Jan 13 13:48:56 2013 -0600
@@ -191,6 +191,12 @@
 #except
 __FATOTWOBIT_BIN__
 #end try
+gmap_bin = #slurp
+#try
+$ref_dict['gmap_bin']
+#except
+__GMAP_BIN__
+#end try
 r_bin = #slurp
 #try
 $ref_dict['r_bin']
@@ -552,6 +558,7 @@
 if `grep __BOWTIE_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
 if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
 if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
+if `grep __GMAP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi
 if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
 if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi