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Make and Clusters

From: Shaun Jackman
Subject: Make and Clusters
Date: Tue, 10 Oct 2017 09:55:37 -0700

Hi, David. Two options:

1. Use Biomake, which is mostly compatible with GNU Make, and supports 
submitting jobs to Slurm.

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

qsub=qsub -sync y

qsub=qsub -Wblock=true

I haven't tried but it seems possible that you could set the variables SHELL 
andĀ .SHELLFLAGS to run qsub for every command. SeeĀ


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