--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config_sub.sh	Mon May 20 15:25:03 2019 -0400
@@ -0,0 +1,29 @@
+#!/bin/bash
+## substitute pathnames into config file
+#!/bin/bash
+SAMTOOLS_BIN=`which samtools`
+BOWTIE_BIN=`which bowtie`
+BOWTIE_BUILD_BIN=`which bowtie-build`
+BLAT_BIN=`which blat`
+FATOTWOBIT_BIN=`which faToTwoBit`
+GMAP_BIN=`which gmap`
+GMAP_BUILD_BIN=`which gmap_build`
+GMAP_SETUP_BIN=$GMAP_BUILD_BIN
+R_BIN=`which R`
+RSCRIPT_BIN=`which Rscript`
+DEFUSE_BIN=`which defuse_run.pl`
+DEFUSE_PATH=`python -c "import os.path;  print(os.path.dirname(os.path.dirname(os.path.realpath(\"$DEFUSE_BIN\"))))"`
+cat $1 | sed "s#__DEFUSE_PATH__#${DEFUSE_PATH}#" | \
+sed "s#__SAMTOOLS_BIN__#${SAMTOOLS_BIN}#" | \
+sed "s#__BOWTIE_BIN__#${BOWTIE_BIN}#" | \
+sed "s#__BOWTIE_BUILD_BIN__#${BOWTIE_BUILD_BIN}#" | \
+sed "s#__BLAT_BIN__#${BLAT_BIN}#"| \
+sed "s#__FATOTWOBIT_BIN__#${FATOTWOBIT_BIN}#" | \
+sed "s#__GMAP_BIN__#${GMAP_BIN}#" | \
+sed "s#^gmap_setup_bin#gmap_build_bin#" | \
+sed "s#__GMAP_SETUP_BIN__#${GMAP_SETUP_BIN}#" | \
+sed "s#__GMAP_BUILD_BIN__#${GMAP_BUILD_BIN}#" | \
+sed "s#__R_BIN__#${R_BIN}#" | \
+sed "s#__RSCRIPT_BIN__#${RSCRIPT_BIN}#" > $2
+export DATASET_DIRECTORY=`grep '^dataset_directory' $1 | awk '{print \$NF}'`
+echo "$DATASET_DIRECTORY"