def chipqc(bam_file, sample, out_dir):
    """Attempt code to run ChIPQC bioconductor packate in one sample"""
    sample_name = dd.get_sample_name(sample)
    logger.warning("ChIPQC is unstable right now, if it breaks, turn off the tool.")
    if utils.file_exists(out_dir):
        return _get_output(out_dir)
    with tx_tmpdir() as tmp_dir:
        rcode = _sample_template(sample, tmp_dir)
        if rcode:
            # local_sitelib = utils.R_sitelib()
            rscript = utils.Rscript_cmd()
            do.run([rscript, "--no-environ", rcode], "ChIPQC in %s" % sample_name, log_error=False)
            shutil.move(tmp_dir, out_dir)
    return _get_output(out_dir)
def chipqc ( bam_file , sample , out_dir ) : sample_name = dd . get_sample_name ( sample ) logger . warning ( "ChIPQC is unstable right now, if it breaks, turn off the tool." ) if utils . file_exists ( out_dir ) : return _get_output ( out_dir ) with tx_tmpdir ( ) as tmp_dir : rcode = _sample_template ( sample , tmp_dir ) if rcode : rscript = utils . Rscript_cmd ( ) do . run ( [ rscript , "--no-environ" , rcode ] , "ChIPQC in %s" % sample_name , log_error = False ) shutil . move ( tmp_dir , out_dir ) return _get_output ( out_dir )
Attempt code to run ChIPQC bioconductor packate in one sample