Make and Clusters

[Shaun Jackman]

Hi, David. Two options:

1. Use Biomake, which is mostly compatible with GNU Make, and supports 
submitting jobs to Slurm.
https://github.com/evoldoers/biomake

It can be installed with Linuxbrew on Linux or Homebrew on macOS.
brew install homebrew/science/biomake

2. Precede each command that you want to run on the cluster with $qsub. Set 
that variable qsub to submit a job and wait for it to finish. For example:

# Slurm
qsub=sbatch --wait

# SGE
qsub=qsub -sync y

# PBS
qsub=qsub -Wblock=true

I haven't tried but it seems possible that you could set the variables SHELL 
and .SHELLFLAGS to run qsub for every command. See 
https://www.gnu.org/software/make/manual/html_node/Choosing-the-Shell.html

Cheers,
Shaun