Mercurial > repos > iuc > jbrowse
changeset 45:a6e57ff585c0 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 80fbf6800feb0bb02c047d37e97b7a12e9c68f4c"
| author | iuc |
|---|---|
| date | Fri, 23 Apr 2021 11:37:36 +0000 |
| parents | 87dc4ce42281 |
| children | |
| files | jbrowse.py |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/jbrowse.py Thu Apr 22 20:26:48 2021 +0000 +++ b/jbrowse.py Fri Apr 23 11:37:36 2021 +0000 @@ -605,7 +605,7 @@ def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): dest = os.path.join('data', 'raw', trackData['label'] + '.bam') self.symlink_or_copy(os.path.realpath(data), dest) - if bam_index is not None: + if bam_index is not None and os.path.exists(os.path.realpath(bam_index)): # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest self.subprocess_check_call(['cp', os.path.realpath(bam_index), dest + '.bai']) else: @@ -614,7 +614,7 @@ # => no index generated by galaxy, but there might be one next to the symlink target # this trick allows to skip the bam sorting made by galaxy if already done outside if os.path.exists(os.path.realpath(data) + '.bai'): - self.symlink_or_copy(os.path.realpath(data) + '.bai', dest) + self.symlink_or_copy(os.path.realpath(data) + '.bai', dest + '.bai') else: log.warn('Could not find a bam index (.bai file) for %s', data)