Mercurial > repos > jjohnson > defuse
comparison datamanager_create_reference.xml @ 15:b67c24d902aa draft
Uploaded
author | jjohnson |
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date | Tue, 12 Dec 2017 12:00:24 -0500 |
parents | 3a4876d01c7e |
children | bdd93719cede |
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14:038a5210392a | 15:b67c24d902aa |
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189 bowtie_build_bin = __BOWTIE_BUILD_BIN__ | 189 bowtie_build_bin = __BOWTIE_BUILD_BIN__ |
190 blat_bin = __BLAT_BIN__ | 190 blat_bin = __BLAT_BIN__ |
191 fatotwobit_bin = __FATOTWOBIT_BIN__ | 191 fatotwobit_bin = __FATOTWOBIT_BIN__ |
192 gmap_bin = __GMAP_BIN__ | 192 gmap_bin = __GMAP_BIN__ |
193 gmap_setup_bin = __GMAP_SETUP_BIN__ | 193 gmap_setup_bin = __GMAP_SETUP_BIN__ |
194 gmap_build_bin = __GMAP_BUILD_BIN__ | |
194 r_bin = __R_BIN__ | 195 r_bin = __R_BIN__ |
195 rscript_bin = __RSCRIPT_BIN__ | 196 rscript_bin = __RSCRIPT_BIN__ |
196 | 197 |
197 #raw | 198 #raw |
198 # Directory where you want your dataset | 199 # Directory where you want your dataset |
259 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 | 260 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 |
260 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 | 261 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 |
261 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 | 262 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 |
262 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 | 263 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 |
263 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 | 264 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 |
265 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 | |
264 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 | 266 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 |
265 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 | |
266 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 | |
267 ## copy config to output | 267 ## copy config to output |
268 cp $defuse_config \$1/defuse_config.txt | 268 cp $defuse_config \$1/defuse_config.txt |
269 ## Run the create_reference_dataset.pl | 269 ## Run the create_reference_dataset.pl |
270 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config | 270 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config |
271 </configfile> | 271 </configfile> |