Mercurial > repos > fubar > jbrowse2
comparison autogenJB2.py @ 53:bdfa6a7c4543 draft
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 |
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| 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 |