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comparison create_reference_dataset.xml @ 35:a004033614d4

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Change for extra_files_path
author Jim Johnson <jj@umn.edu>
date Mon, 13 Oct 2014 15:42:10 -0500
parents 3099cec648e7
children 74de1ccc51db 225750bf3770
comparison
equal deleted inserted replaced
34:3099cec648e7 35:a004033614d4
147 ucsc_genome_version = $genome.ucsc_genome_version 147 ucsc_genome_version = $genome.ucsc_genome_version
148 ncbi_organism = $genome.ncbi_organism 148 ncbi_organism = $genome.ncbi_organism
149 ncbi_prefix = $genome.ncbi_prefix 149 ncbi_prefix = $genome.ncbi_prefix
150 150
151 # Directory where you want your dataset 151 # Directory where you want your dataset
152 dataset_directory = $config_txt.extra_files_path 152 dataset_directory = $config_txt.dataset.extra_files_path
153 153
154 #raw 154 #raw
155 # Input genome and gene models 155 # Input genome and gene models
156 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf 156 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf
157 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa 157 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa
245 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 245 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
246 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 246 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
247 ## copy config to output 247 ## copy config to output
248 cp $defuse_config $config_txt 248 cp $defuse_config $config_txt
249 ## make a data_dir and ln -s the input fastq 249 ## make a data_dir and ln -s the input fastq
250 mkdir -p $config_txt.extra_files_path 250 mkdir -p $config_txt.dataset.extra_files_path
251 ## create_reference_dataset.pl 251 ## create_reference_dataset.pl
252 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config 252 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config
253 </configfile> 253 </configfile>
254 </configfiles> 254 </configfiles>
255 255