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45
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1 #!/bin/bash
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2 ## substitute pathnames into config file
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3 #!/bin/bash
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4 SAMTOOLS_BIN=`which samtools`
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5 BOWTIE_BIN=`which bowtie`
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6 BOWTIE_BUILD_BIN=`which bowtie-build`
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7 BLAT_BIN=`which blat`
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8 FATOTWOBIT_BIN=`which faToTwoBit`
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9 GMAP_BIN=`which gmap`
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10 GMAP_BUILD_BIN=`which gmap_build`
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11 GMAP_SETUP_BIN=$GMAP_BUILD_BIN
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12 R_BIN=`which R`
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13 RSCRIPT_BIN=`which Rscript`
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46
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14 DEFUSE_BIN=`which defuse_run.pl`
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15 DEFUSE_PATH=`python -c "import os.path; print os.path.dirname(os.path.dirname(os.path.realpath(\"$DEFUSE_BIN\")))"`
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16 cat $1 | sed "s#__DEFUSE_PATH__#${DEFUSE_PATH}#" | \
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17 sed "s#__SAMTOOLS_BIN__#${SAMTOOLS_BIN}#" | \
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18 sed "s#__BOWTIE_BIN__#${BOWTIE_BIN}#" | \
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45
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19 sed "s#__BOWTIE_BUILD_BIN__#${BOWTIE_BUILD_BIN}#" | \
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20 sed "s#__BLAT_BIN__#${BLAT_BIN}#"| \
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21 sed "s#__FATOTWOBIT_BIN__#${FATOTWOBIT_BIN}#" | \
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22 sed "s#__GMAP_BIN__#${GMAP_BIN}#" | \
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23 sed "s#^gmap_setup_bin#gmap_build_bin#" | \
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24 sed "s#__GMAP_SETUP_BIN__#${GMAP_SETUP_BIN}#" | \
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25 sed "s#__GMAP_BUILD_BIN__#${GMAP_BUILD_BIN}#" | \
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26 sed "s#__R_BIN__#${R_BIN}#" | \
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27 sed "s#__RSCRIPT_BIN__#${RSCRIPT_BIN}#" > $2
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46
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28 export DATASET_DIRECTORY=`grep '^dataset_directory' $1 | awk '{print \$NF}'`
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29 echo "$DATASET_DIRECTORY"
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