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comparison defuse.xml @ 9:9f30de0ff090 draft

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Add gmap_setup_bin and gmap_index_directory to defuse.xml config file generation
author Jim Johnson <jj@umn.edu>
date Mon, 14 Jan 2013 11:26:17 -0600
parents 57841f58676f
children f65857c1b92e
comparison
equal deleted inserted replaced
8:57841f58676f 9:9f30de0ff090
195 #try 195 #try
196 $ref_dict['gmap_bin'] 196 $ref_dict['gmap_bin']
197 #except 197 #except
198 __GMAP_BIN__ 198 __GMAP_BIN__
199 #end try 199 #end try
200 gmap_bin = #slurp
201 #try
202 $ref_dict['gmap_bin']
203 #except
204 __GMAP_BIN__
205 #end try
206 gmap_setup_bin = #slurp
207 #try
208 $ref_dict['gmap_setup_bin']
209 #except
210 __GMAP_SETUP_BIN__
211 #end try
200 r_bin = #slurp 212 r_bin = #slurp
201 #try 213 #try
202 $ref_dict['r_bin'] 214 $ref_dict['r_bin']
203 #except 215 #except
204 __R_BIN__ 216 __R_BIN__
207 #try 219 #try
208 $ref_dict['rscript_bin'] 220 $ref_dict['rscript_bin']
209 #except 221 #except
210 __RSCRIPT_BIN__ 222 __RSCRIPT_BIN__
211 #end try 223 #end try
224
225 # Directory where you want your dataset
226 gmap_index_directory = #slurp
227 #try
228 $ref_dict['gmap_index_directory']
229 #except
230 $(dataset_directory)/gmap
231 #end try
232
212 233
213 #raw 234 #raw
214 # Dataset files 235 # Dataset files
215 dataset_prefix = $(dataset_directory)/defuse 236 dataset_prefix = $(dataset_directory)/defuse
216 chromosome_prefix = $(dataset_prefix).dna.chromosomes 237 chromosome_prefix = $(dataset_prefix).dna.chromosomes
557 if `grep __BOWTIE_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi 578 if `grep __BOWTIE_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
558 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 579 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
559 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 580 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
560 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 581 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
561 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 582 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
583 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
562 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 584 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
563 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 585 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
564 586
565 587
566 ## copy config to output 588 ## copy config to output