# HG changeset patch
# User jjohnson
# Date 1513098024 18000
# Node ID b67c24d902aac3f17e977bd8612155dafe401320
# Parent  038a5210392aa7216ad987489f448bd5c8dd9972
Uploaded

diff -r 038a5210392a -r b67c24d902aa create_reference_dataset.xml
--- a/create_reference_dataset.xml	Tue Dec 12 10:02:00 2017 -0500
+++ b/create_reference_dataset.xml	Tue Dec 12 12:00:24 2017 -0500
@@ -190,6 +190,7 @@
 fatotwobit_bin = __FATOTWOBIT_BIN__
 gmap_bin = __GMAP_BIN__
 gmap_setup_bin = __GMAP_SETUP_BIN__
+gmap_build_bin = __GMAP_BUILD_BIN__
 r_bin = __R_BIN__
 rscript_bin = __RSCRIPT_BIN__
 
@@ -259,6 +260,7 @@
 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 __GMAP_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BUILD_BIN=`which gmap_build`;then sed -i'.tmp' "s#__GMAP_BUILD_BIN__#\${GMAP_BUILD_BIN}#" $defuse_config; fi
 if `grep __GMAP_INDEX_DIR__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $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
diff -r 038a5210392a -r b67c24d902aa datamanager_create_reference.xml
--- a/datamanager_create_reference.xml	Tue Dec 12 10:02:00 2017 -0500
+++ b/datamanager_create_reference.xml	Tue Dec 12 12:00:24 2017 -0500
@@ -191,6 +191,7 @@
 fatotwobit_bin = __FATOTWOBIT_BIN__
 gmap_bin = __GMAP_BIN__
 gmap_setup_bin = __GMAP_SETUP_BIN__
+gmap_build_bin = __GMAP_BUILD_BIN__
 r_bin = __R_BIN__
 rscript_bin = __RSCRIPT_BIN__
 
@@ -261,9 +262,8 @@
 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 __GMAP_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BUILD_BIN=`which gmap_build`;then sed -i'.tmp' "s#__GMAP_BUILD_BIN__#\${GMAP_BUILD_BIN}#" $defuse_config; fi
 if `grep __GMAP_INDEX_DIR__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $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
 ## copy config to output
 cp $defuse_config \$1/defuse_config.txt
 ## Run the create_reference_dataset.pl