Mercurial > repos > iuc > jbrowse
comparison jbrowse.py @ 44:87dc4ce42281 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
| author | iuc |
|---|---|
| date | Thu, 22 Apr 2021 20:26:48 +0000 |
| parents | 8774b28235bb |
| children | a6e57ff585c0 |
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| 43:4542035c1075 | 44:87dc4ce42281 |
|---|---|
| 603 self._add_track_json(trackData) | 603 self._add_track_json(trackData) |
| 604 | 604 |
| 605 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): | 605 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): |
| 606 dest = os.path.join('data', 'raw', trackData['label'] + '.bam') | 606 dest = os.path.join('data', 'raw', trackData['label'] + '.bam') |
| 607 self.symlink_or_copy(os.path.realpath(data), dest) | 607 self.symlink_or_copy(os.path.realpath(data), dest) |
| 608 self.symlink_or_copy(os.path.realpath(bam_index), dest + '.bai') | 608 if bam_index is not None: |
| 609 # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest | |
| 610 self.subprocess_check_call(['cp', os.path.realpath(bam_index), dest + '.bai']) | |
| 611 else: | |
| 612 # Can happen in exotic condition | |
| 613 # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam | |
| 614 # => no index generated by galaxy, but there might be one next to the symlink target | |
| 615 # this trick allows to skip the bam sorting made by galaxy if already done outside | |
| 616 if os.path.exists(os.path.realpath(data) + '.bai'): | |
| 617 self.symlink_or_copy(os.path.realpath(data) + '.bai', dest) | |
| 618 else: | |
| 619 log.warn('Could not find a bam index (.bai file) for %s', data) | |
| 609 | 620 |
| 610 url = os.path.join('raw', trackData['label'] + '.bam') | 621 url = os.path.join('raw', trackData['label'] + '.bam') |
| 611 trackData.update({ | 622 trackData.update({ |
| 612 "urlTemplate": url, | 623 "urlTemplate": url, |
| 613 "type": "JBrowse/View/Track/Alignments2", | 624 "type": "JBrowse/View/Track/Alignments2", |