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.")
