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comparison config_sub.sh @ 46:e500b50b72fd draft default tip

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author jjohnson
date Thu, 19 Oct 2017 10:05:54 -0400
parents aedaa66483f1
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45:aedaa66483f1 46:e500b50b72fd
9 GMAP_BIN=`which gmap` 9 GMAP_BIN=`which gmap`
10 GMAP_BUILD_BIN=`which gmap_build` 10 GMAP_BUILD_BIN=`which gmap_build`
11 GMAP_SETUP_BIN=$GMAP_BUILD_BIN 11 GMAP_SETUP_BIN=$GMAP_BUILD_BIN
12 R_BIN=`which R` 12 R_BIN=`which R`
13 RSCRIPT_BIN=`which Rscript` 13 RSCRIPT_BIN=`which Rscript`
14 14 DEFUSE_BIN=`which defuse_run.pl`
15 cat $1 | sed "s#__SAMTOOLS_BIN__#${SAMTOOLS_BIN}#"| \ 15 DEFUSE_PATH=`python -c "import os.path; print os.path.dirname(os.path.dirname(os.path.realpath(\"$DEFUSE_BIN\")))"`
16 sed "s#__BOWTIE_BIN__#${BOWTIE_BIN}#"| \ 16 cat $1 | sed "s#__DEFUSE_PATH__#${DEFUSE_PATH}#" | \
17 sed "s#__SAMTOOLS_BIN__#${SAMTOOLS_BIN}#" | \
18 sed "s#__BOWTIE_BIN__#${BOWTIE_BIN}#" | \
17 sed "s#__BOWTIE_BUILD_BIN__#${BOWTIE_BUILD_BIN}#" | \ 19 sed "s#__BOWTIE_BUILD_BIN__#${BOWTIE_BUILD_BIN}#" | \
18 sed "s#__BLAT_BIN__#${BLAT_BIN}#"| \ 20 sed "s#__BLAT_BIN__#${BLAT_BIN}#"| \
19 sed "s#__FATOTWOBIT_BIN__#${FATOTWOBIT_BIN}#" | \ 21 sed "s#__FATOTWOBIT_BIN__#${FATOTWOBIT_BIN}#" | \
20 sed "s#__GMAP_BIN__#${GMAP_BIN}#" | \ 22 sed "s#__GMAP_BIN__#${GMAP_BIN}#" | \
21 sed "s#^gmap_setup_bin#gmap_build_bin#" | \ 23 sed "s#^gmap_setup_bin#gmap_build_bin#" | \
22 sed "s#__GMAP_SETUP_BIN__#${GMAP_SETUP_BIN}#" | \ 24 sed "s#__GMAP_SETUP_BIN__#${GMAP_SETUP_BIN}#" | \
23 sed "s#__GMAP_BUILD_BIN__#${GMAP_BUILD_BIN}#" | \ 25 sed "s#__GMAP_BUILD_BIN__#${GMAP_BUILD_BIN}#" | \
24 sed "s#__R_BIN__#${R_BIN}#" | \ 26 sed "s#__R_BIN__#${R_BIN}#" | \
25 sed "s#__RSCRIPT_BIN__#${RSCRIPT_BIN}#" > $2 27 sed "s#__RSCRIPT_BIN__#${RSCRIPT_BIN}#" > $2
26 28 export DATASET_DIRECTORY=`grep '^dataset_directory' $1 | awk '{print \$NF}'`
27 ## if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi 29 echo "$DATASET_DIRECTORY"