lambda x: "../rnaseq/ref-transcripts-mask.gtf") resource_dict = tz.update_in( resource_dict, index, lambda x: "../rnaseq/tophat/%s_transcriptome.ver" % args.build) resource_dict = tz.update_in( resource_dict, refflat, lambda x: "../rnaseq/ref-transcripts.refFlat") resource_dict = tz.update_in( resource_dict, dexseq, lambda x: "../rnaseq/ref-transcripts.dexseq.gff3") resource_dict = tz.update_in(resource_dict, rRNA_fa, lambda x: "../rnaseq/rRNA.fa") if args.mirbase: srna_gtf = ["srnaseq", "srna-transcripts"] srna_mirbase = ["srnaseq", "mirbase"] resource_dict = tz.update_in( resource_dict, srna_gtf, lambda x: "../srnaseq/srna-transcripts.gtf") resource_dict = tz.update_in(resource_dict, srna_mirbase, lambda x: "../srnaseq/hairpin.fa") # write out resource dictionarry with file_transaction(resource_file) as tx_resource_file: with open(tx_resource_file, "w") as out_handle: out_handle.write(yaml.dump(resource_dict, default_flow_style=False)) print "Updating Galaxy .loc files." galaxy_base = os.path.join(_get_data_dir(), "galaxy") for index, index_file in indexed.items(): loc.update_loc_file(galaxy_base, index, args.build, index_file)
lambda x: "../rnaseq/ref-transcripts.gtf") resource_dict = tz.update_in(resource_dict, mask, lambda x: "../rnaseq/ref-transcripts-mask.gtf") resource_dict = tz.update_in(resource_dict, index, lambda x: "../rnaseq/tophat/%s_transcriptome.ver" % args.build) resource_dict = tz.update_in(resource_dict, refflat, lambda x: "../rnaseq/ref-transcripts.refFlat") resource_dict = tz.update_in(resource_dict, dexseq, lambda x: "../rnaseq/ref-transcripts.dexseq.gff3") resource_dict = tz.update_in(resource_dict, rRNA_fa, lambda x: "../rnaseq/rRNA.fa") if args.mirbase: srna_gtf = ["srnaseq", "srna_transcripts"] srna_mirbase = ["srnaseq", "mirbase_hairpin"] resource_dict = tz.update_in(resource_dict, srna_gtf, lambda x: "../srnaseq/srna-transcripts.gtf") resource_dict = tz.update_in(resource_dict, srna_mirbase, lambda x: "../srnaseq/hairpin.fa") # write out resource dictionarry with file_transaction(resource_file) as tx_resource_file: with open(tx_resource_file, "w") as out_handle: out_handle.write(yaml.dump(resource_dict, default_flow_style=False)) print("Updating Galaxy .loc files.") galaxy_base = os.path.join(_get_data_dir(), "galaxy") for index, index_file in indexed.items(): if index_file: loc.update_loc_file(galaxy_base, index, args.build, index_file) print("Genome installation complete.")