comparison jbrowse.py @ 44:87dc4ce42281 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"

43:4542035c1075

        self._add_track_json(trackData)

    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)
        self.symlink_or_copy(os.path.realpath(bam_index), dest + '.bai')

        url = os.path.join('raw', trackData['label'] + '.bam')
        trackData.update({
            "urlTemplate": url,
            "type": "JBrowse/View/Track/Alignments2",

44:87dc4ce42281

        self._add_track_json(trackData)

    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:
            # 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:
            # Can happen in exotic condition
            # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam
            #      => 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)
            else:
                log.warn('Could not find a bam index (.bai file) for %s', data)

        url = os.path.join('raw', trackData['label'] + '.bam')
        trackData.update({
            "urlTemplate": url,
            "type": "JBrowse/View/Track/Alignments2",