Mercurial > repos > iuc > jbrowse
comparison jbrowse.py @ 41:8774b28235bb draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
| author | iuc |
|---|---|
| date | Thu, 31 Dec 2020 16:00:42 +0000 |
| parents | 17359b808b01 |
| children | 87dc4ce42281 |
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| 40:17359b808b01 | 41:8774b28235bb |
|---|---|
| 398 return subprocess.check_output(command, cwd=self.outdir) | 398 return subprocess.check_output(command, cwd=self.outdir) |
| 399 | 399 |
| 400 def _jbrowse_bin(self, command): | 400 def _jbrowse_bin(self, command): |
| 401 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command)) | 401 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command)) |
| 402 | 402 |
| 403 def symlink_or_copy(self, src, dest): | |
| 404 if 'GALAXY_JBROWSE_SYMLINKS' in os.environ and bool(os.environ['GALAXY_JBROWSE_SYMLINKS']): | |
| 405 cmd = ['ln', '-s', src, dest] | |
| 406 else: | |
| 407 cmd = ['cp', src, dest] | |
| 408 | |
| 409 return self.subprocess_check_call(cmd) | |
| 410 | |
| 403 def process_genomes(self): | 411 def process_genomes(self): |
| 404 for genome_node in self.genome_paths: | 412 for genome_node in self.genome_paths: |
| 405 # We only expect one input genome per run. This for loop is just | 413 # We only expect one input genome per run. This for loop is just |
| 406 # easier to write than the alternative / catches any possible | 414 # easier to write than the alternative / catches any possible |
| 407 # issues. | 415 # issues. |
| 505 if blastOpts.get('index', 'false') == 'true': | 513 if blastOpts.get('index', 'false') == 'true': |
| 506 self.tracksToIndex.append("%s" % trackData['label']) | 514 self.tracksToIndex.append("%s" % trackData['label']) |
| 507 | 515 |
| 508 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): | 516 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): |
| 509 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') | 517 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') |
| 510 cmd = ['cp', data, dest] | 518 self.symlink_or_copy(os.path.realpath(data), dest) |
| 511 self.subprocess_check_call(cmd) | |
| 512 | 519 |
| 513 url = os.path.join('raw', trackData['label'] + '.bw') | 520 url = os.path.join('raw', trackData['label'] + '.bw') |
| 514 trackData.update({ | 521 trackData.update({ |
| 515 "urlTemplate": url, | 522 "urlTemplate": url, |
| 516 "storeClass": "JBrowse/Store/SeqFeature/BigWig", | 523 "storeClass": "JBrowse/Store/SeqFeature/BigWig", |
| 533 def add_bigwig_multiple(self, data, trackData, wiggleOpts, **kwargs): | 540 def add_bigwig_multiple(self, data, trackData, wiggleOpts, **kwargs): |
| 534 | 541 |
| 535 urls = [] | 542 urls = [] |
| 536 for idx, bw in enumerate(data): | 543 for idx, bw in enumerate(data): |
| 537 dest = os.path.join('data', 'raw', trackData['label'] + '_' + str(idx) + '.bw') | 544 dest = os.path.join('data', 'raw', trackData['label'] + '_' + str(idx) + '.bw') |
| 538 cmd = ['ln', '-s', bw[1], dest] | 545 self.symlink_or_copy(bw[1], dest) |
| 539 self.subprocess_check_call(cmd) | |
| 540 | 546 |
| 541 urls.append({"url": os.path.join('raw', trackData['label'] + '_' + str(idx) + '.bw'), "name": str(idx + 1) + ' - ' + bw[0]}) | 547 urls.append({"url": os.path.join('raw', trackData['label'] + '_' + str(idx) + '.bw'), "name": str(idx + 1) + ' - ' + bw[0]}) |
| 542 | 548 |
| 543 trackData.update({ | 549 trackData.update({ |
| 544 "urlTemplates": urls, | 550 "urlTemplates": urls, |
| 596 | 602 |
| 597 self._add_track_json(trackData) | 603 self._add_track_json(trackData) |
| 598 | 604 |
| 599 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): | 605 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): |
| 600 dest = os.path.join('data', 'raw', trackData['label'] + '.bam') | 606 dest = os.path.join('data', 'raw', trackData['label'] + '.bam') |
| 601 cmd = ['ln', '-s', os.path.realpath(data), dest] | 607 self.symlink_or_copy(os.path.realpath(data), dest) |
| 602 self.subprocess_check_call(cmd) | 608 self.symlink_or_copy(os.path.realpath(bam_index), dest + '.bai') |
| 603 | |
| 604 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai'] | |
| 605 self.subprocess_check_call(cmd) | |
| 606 | 609 |
| 607 url = os.path.join('raw', trackData['label'] + '.bam') | 610 url = os.path.join('raw', trackData['label'] + '.bam') |
| 608 trackData.update({ | 611 trackData.update({ |
| 609 "urlTemplate": url, | 612 "urlTemplate": url, |
| 610 "type": "JBrowse/View/Track/Alignments2", | 613 "type": "JBrowse/View/Track/Alignments2", |