--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark_deduplicate_wrapper.py	Wed Aug 22 08:09:42 2018 -0400
@@ -0,0 +1,81 @@
+#!/usr/bin/python
+
+import argparse
+import logging
+import os
+import shutil
+import subprocess
+import sys
+import signal
+import tempfile
+from glob import glob
+
+
+def stop_err(logger, msg):
+    logger.critical(msg)
+    sys.exit(1)
+
+
+def restore_sigpipe():
+    """
+    Needed to handle samtools view
+    """
+    signal.signal(signal.SIGPIPE, signal.SIG_DFL)
+
+
+def log_subprocess_output(logger, pipe):
+    for line in iter(pipe.readline, b''):
+        logger.debug(line.decode().rstrip())
+
+
+def get_arg():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--single_or_paired',  dest='single_or_paired')
+    parser.add_argument('--input', dest='input', metavar='input')
+    parser.add_argument('--output_report', dest='output_report', metavar='output_report')
+    parser.add_argument('--output_bam', dest='output_bam', metavar='output_report')
+    parser.add_argument('--log_report', dest='log_report', metavar='log_filename', type=str)
+    args = parser.parse_args()
+    return args
+
+
+def __main__():
+    args = get_arg()
+
+    logger = logging.getLogger('bismark_deduplicate_wrapper')
+    logger.setLevel(logging.DEBUG)
+    ch = logging.StreamHandler(sys.stdout)
+    if args.log_report:
+        ch.setLevel(logging.WARNING)
+        handler = logging.FileHandler(args.log_report)
+        handler.setLevel(logging.DEBUG)
+        logger.addHandler(handler)
+    else:
+        ch.setLevel(logging.DEBUG)
+    logger.addHandler(ch)
+
+    # ensure the input has a .bam suffix
+    tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='')
+    os.chdir(tmp_dir)
+    default_reads_name = 'submitted_reads.bam'
+    os.symlink(args.input, default_reads_name)
+
+    single_or_paired = '-s' if args.single_or_paired == 'single' else '-p'
+    cmd = ['deduplicate_bismark', single_or_paired, default_reads_name, '--bam']
+    logger.info("Deduplicating with: '%s'", " ".join(cmd))
+    process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
+                               preexec_fn=restore_sigpipe)
+    proc_out, proc_err = process.communicate()
+    logger.info(proc_out)
+    if process.returncode != 0:
+        stop_err(logger, "Bismark deduplication error (also check the log file if any)!\n%s" % proc_err)
+
+    deduplicated_out_name = 'submitted_reads.deduplicated.bam'
+    deduplicated_report_name = 'submitted_reads.deduplication_report.txt'
+    logger.debug("Moving '%s' to galaxy: '%s'.", deduplicated_out_name, args.output_bam)
+    shutil.move(deduplicated_out_name, args.output_bam )
+    logger.debug("Moving '%s' to galaxy: '%s'.", deduplicated_report_name, args.output_report)
+    shutil.move('submitted_reads.deduplication_report.txt', args.output_report)
+    logger.debug("Done.")
+
+if __name__=="__main__": __main__()
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