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comparison create_reference_dataset.xml @ 17:c3167ccca38c draft default tip

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit d2317dff5a89016f18038b97d057f47d949e7808-dirty
author jjohnson
date Sat, 26 Jan 2019 12:53:08 -0500
parents bdd93719cede
children
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16:bdd93719cede 17:c3167ccca38c
162 ucsc_genome_version = $genome.ucsc_genome_version 162 ucsc_genome_version = $genome.ucsc_genome_version
163 ncbi_organism = $genome.ncbi_organism 163 ncbi_organism = $genome.ncbi_organism
164 ncbi_prefix = $genome.ncbi_prefix 164 ncbi_prefix = $genome.ncbi_prefix
165 165
166 # Directory where you want your dataset 166 # Directory where you want your dataset
167 dataset_directory = $config_txt.dataset.extra_files_path 167 dataset_directory = $config_txt.extra_files_path
168 168
169 #raw 169 #raw
170 # Input genome and gene models 170 # Input genome and gene models
171 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf 171 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf
172 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa 172 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa
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 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 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 $config_txt 268 cp $defuse_config $config_txt
269 ## make a data_dir and ln -s the input fastq 269 ## make a data_dir and ln -s the input fastq
270 mkdir -p $config_txt.dataset.extra_files_path 270 mkdir -p $config_txt.files_path
271 ## create_reference_dataset.pl 271 ## create_reference_dataset.pl
272 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config 272 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config
273 </configfile> 273 </configfile>
274 </configfiles> 274 </configfiles>
275 275