# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1358542600 21600
# Node ID f4eadbd2e7c1e217b3324986686c08838e15af09
# Parent  5545ec69acbdb02557af6fb2254797f4759a78b1
Add gmap_setup_bin and gmap_index_directory to defuse.xml config file generation

diff -r 5545ec69acbd -r f4eadbd2e7c1 defuse.xml
--- a/defuse.xml	Mon Jan 07 12:44:55 2013 -0600
+++ b/defuse.xml	Fri Jan 18 14:56:40 2013 -0600
@@ -191,6 +191,24 @@
 #except
 __FATOTWOBIT_BIN__
 #end try
+gmap_bin = #slurp
+#try
+$ref_dict['gmap_bin']
+#except
+__GMAP_BIN__
+#end try
+gmap_bin = #slurp
+#try
+$ref_dict['gmap_bin']
+#except
+__GMAP_BIN__
+#end try
+gmap_setup_bin = #slurp
+#try
+$ref_dict['gmap_setup_bin']
+#except
+__GMAP_SETUP_BIN__
+#end try
 r_bin = #slurp
 #try
 $ref_dict['r_bin']
@@ -204,6 +222,14 @@
 __RSCRIPT_BIN__
 #end try
 
+# Directory where you want your dataset
+gmap_index_directory = #slurp
+#try
+$ref_dict['gmap_index_directory']
+#except
+\$(dataset_directory)/gmap
+#end try
+
 #raw
 # Dataset files
 dataset_prefix       = $(dataset_directory)/defuse
@@ -552,6 +578,8 @@
 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 __GMAP_SETUP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_SETUP_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_SETUP_BIN__#\${GMAP_SETUP_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