Mercurial > repos > fubar > jbrowse2

comparison autogenJB2.py @ 93:4c517a0041a8 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
author fubar
date Wed, 24 Apr 2024 02:29:32 +0000
parents 3c4db8203fad
children 74074746ccd8
comparison
equal deleted inserted replaced
92:3c4db8203fad 93:4c517a0041a8
141 os.path.realpath(track[0]), 141 os.path.realpath(track[0]),
142 ] 142 ]
143 sys.stdout.write("#### calling %s" % " ".join(cmd)) 143 sys.stdout.write("#### calling %s" % " ".join(cmd))
144 jc.subprocess_check_call(cmd) 144 jc.subprocess_check_call(cmd)
145 track_conf.update( 145 track_conf.update(
146 {"conf": {"options": {"bam": {"bam_index": " %s:%s," % (tpath,ipath)}}}} 146 {"conf": {"options": {"bam": {"bam_index": " %s ~ %s," % (tpath,ipath)}}}}
147 ) 147 )
148 elif trext == "cram": 148 elif trext == "cram":
149 ipath = track[3] 149 ipath = track[3]
150 if not os.path.exists(ipath): 150 if not os.path.exists(ipath):
151 ipath = os.path.realpath( 151 ipath = os.path.realpath(
159 ipath, 159 ipath,
160 os.path.realpath(track[0]), 160 os.path.realpath(track[0]),
161 ] 161 ]
162 jc.subprocess_check_call(cmd) 162 jc.subprocess_check_call(cmd)
163 track_conf.update( 163 track_conf.update(
164 {"conf": {"options": {"cram": {"cram_index": "%s:%s," % (tpath, ipath)}}}} 164 {"conf": {"options": {"cram": {"cram_index": "%s ~ %s," % (tpath, ipath)}}}}
165 ) 165 )
166 track_conf["path"] = tpath 166 track_conf["path"] = tpath
167 track_conf["format"] = trext 167 track_conf["format"] = trext
168 track_conf["name"] = trackname 168 track_conf["name"] = trackname
169 track_conf["label"] = trackname 169 track_conf["label"] = trackname