pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
20 stars 7 forks source link

Use bash for submission #282

Open nsheff opened 4 years ago

nsheff commented 4 years ago

Awhile ago I ran into an issue using looper in an environment that wasn't running on bash.

This solved the problem. I'm not sure this is what we should do, but wanted to document that if the shell isn't bash, then the config files can't use bash constructs... so we may want to think of a systematic way to handle this.

codecov[bot] commented 4 years ago

Codecov Report

Merging #282 into dev will not change coverage. The diff coverage is 0.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##              dev     #282   +/-   ##
=======================================
  Coverage   18.06%   18.06%           
=======================================
  Files          32       32           
  Lines        4040     4040           
=======================================
  Hits          730      730           
  Misses       3310     3310           
Impacted Files Coverage Δ
looper/conductor.py 15.72% <0.00%> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update dfc806c...9eeecfb. Read the comment docs.

nsheff commented 4 years ago

See #280