Mercurial > repos > fubar > jbrowse2
comparison autogenJB2.py @ 93:4c517a0041a8 draft
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 |
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| 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 |