Mercurial > repos > fubar > jbrowse2
comparison autogenJB2.py @ 92:3c4db8203fad draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78
author | fubar |
---|---|
date | Sun, 21 Apr 2024 04:42:29 +0000 |
parents | 3b2ff9864995 |
children | 4c517a0041a8 |
comparison
equal
deleted
inserted
replaced
91:6246925692cb | 92:3c4db8203fad |
---|---|
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 " % (trackname,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" % (trackname,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 |