Running job arrays on HPC using Singularity and a Docker image

I thought I’d share a little success story. A researcher recently approached me to say he’d been having difficulty getting his bioinformatics workflow (based on this) working on the University of Sheffield’s ShARC HPC cluster and had an urgent need to get it running to meet a pending deadline. He’s primarily using the GATK ‘genome analysis toolkit’. He appealed for help on the GATK forum, members of which suggested that the issue may be due to the way in which GATK was installed.

Running Abaqus 2017 within a Singularity container (with hw-accel graphics)

When I started as a Research Software Engineer at the Uni of Sheffield a year ago I was given a lovely Dell XPS 9550 laptop to work on. The first thing I did was to install Arch Linux on it, which has so far proved to be extremely stable despite the rolling release model and the main Arch repository offering very recent versions of most FOSS packages. Large engineering apps say no to bleeding edge Linux distros However, the one main issue with running Arch at work is that some commercial engineering software supports Linux but not all flavours: there are a fair few commercial packages that are only supported and only really work with RHEL/Centos/SLES and Ubuntu.

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