Mercurial > repos > fubar > jbrowse2

comparison autogenJB2.py @ 53:bdfa6a7c4543 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
author fubar
date Thu, 07 Mar 2024 09:23:06 +0000
parents ae12977c0e5e
children 94264fe60478
comparison
equal deleted inserted replaced
52:ae12977c0e5e 53:bdfa6a7c4543
127 jc.subprocess_check_call(cmd) 127 jc.subprocess_check_call(cmd)
128 track_conf.update({"conf": {"options": {"bam": {"bam_index": ipath}}}}) 128 track_conf.update({"conf": {"options": {"bam": {"bam_index": ipath}}}})
129 elif trext == "cram": 129 elif trext == "cram":
130 ipath = track[3] 130 ipath = track[3]
131 if not os.path.exists(ipath): 131 if not os.path.exists(ipath):
132 jc.logging.info('calling %s' % ' '.join(cmd))
133 ipath = os.path.realpath(os.path.join('./', trackname + '.crai')) 132 ipath = os.path.realpath(os.path.join('./', trackname + '.crai'))
134 cmd = ["samtools", "index", "-c", "-o", ipath, os.path.realpath(track[0])] 133 cmd = ["samtools", "index", "-c", "-o", ipath, os.path.realpath(track[0])]
135 sys.stdout.write('#### calling %s' % ' '.join(cmd))
136 jc.subprocess_check_call(cmd) 134 jc.subprocess_check_call(cmd)
137 track_conf.update({"conf": {"options": {"cram": {"cram_index": ipath}}}}) 135 track_conf.update({"conf": {"options": {"cram": {"cram_index": ipath}}}})
138 track_conf["path"] = tpath 136 track_conf["path"] = tpath
139 track_conf["format"] = trext 137 track_conf["format"] = trext
140 track_conf["name"] = trackname 138 track_conf["name"] = trackname