Mercurial > repos > fubar > jbrowse2

comparison autogenJB2.py @ 113:878c27dfea9d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 45375b64cbc99173525a2b374d71a13e650ce1b0
author bgruening
date Sun, 28 Jul 2024 02:42:43 +0000
parents b1260bca5fdc
children
comparison
equal deleted inserted replaced
112:56f9a6e0fe80 113:878c27dfea9d
90 } 90 }
91 listtracks = trackList 91 listtracks = trackList
92 # foo.paf must have a foo_paf.fasta or fasta.gz to match 92 # foo.paf must have a foo_paf.fasta or fasta.gz to match
93 tnames = [x[2] for x in listtracks] 93 tnames = [x[2] for x in listtracks]
94 texts = [x[1] for x in listtracks] 94 texts = [x[1] for x in listtracks]
95 if len(listtracks) == 0:
96 sys.stderr.write(
97 "Please add at least one track (bam,bed,bigwig,blastxml,cram,gff,hic,maf,paf or vcf) to the collection. No suitable track files for autogenJB2 - nothing to process"
98 )
99 sys.exit(5)
95 for i, track in enumerate(listtracks): 100 for i, track in enumerate(listtracks):
96 track_conf = { 101 track_conf = {
97 "trackfiles": [], 102 "trackfiles": [],
98 "category": "autogenerated", 103 "category": "autogenerated",
99 "assemblyNames": assref_name, 104 "assemblyNames": assref_name,
222 jc.add_default_session(default_session_data) 227 jc.add_default_session(default_session_data)
223 # jc.add_defsess_to_index(default_session_data) 228 # jc.add_defsess_to_index(default_session_data)
224 # jc.text_index() not sure what broke here. 229 # jc.text_index() not sure what broke here.
225 else: 230 else:
226 sys.stderr.write( 231 sys.stderr.write(
227 "Collection has no suitable trackfiles for autogenJB2 - nothing to process" 232 "Please add a fasta genome reference to the collection. No suitable reference fasta for autogenJB2 - nothing to process"
228 ) 233 )