lparsons

#!/usr/bin/env bash

set -Eeuo pipefail
trap cleanup SIGINT SIGTERM ERR EXIT

script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &>/dev/null && pwd -P)

usage() {
  cat <<EOF
Usage: $(basename "${BASH_SOURCE[0]}") [-h] [-v] [-f] -p param_value arg1 [arg2...]

lparsons

diff --git a/src/toil/batchSystems/slurm.py b/src/toil/batchSystems/slurm.py
index 03884b7f..782d9f0c 100644
--- a/src/toil/batchSystems/slurm.py
+++ b/src/toil/batchSystems/slurm.py
@@ -96,8 +96,8 @@ class SlurmBatchSystem(AbstractGridEngineBatchSystem):
                     '-n', # no header
                     '-j', str(slurmJobID), # job
                     '--format', 'State,ExitCode', # specify output columns
-                    '-P', # separate columns with pipes
-                    '-S', '1970-01-01'] # override start time limit

lparsons

Homebrew build logs for vim on "Springdale Linux  release 6.9 (Pisa)"
Build date: 2017-10-04 16:47:28

lparsons

Homebrew build logs for homebrew/science/express on Mac OS X 10.11.5
Build date: 2016-07-12 10:43:52

lparsons

#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" Add simulated 5' UTR regions to GTF records.
    Wrapper script for workaround provided by Joshua Griffin Dunn
    <https://www.linkedin.com/in/joshuagriffindunn>
    https://github.com/joshuagryphon/plastid/issues/3#issuecomment-202572593
"""

import argparse
import logging