darcyabjones/pclust repository overview

⁠pclust

This is the docker repository for running the pclust⁠ pipeline. The pipeline is for clustering and comparing distantly related proteins, with a particular focus of detecting remote homology between fungal effector proteins.

The image contains:

• MMSeqs⁠
• HHSuite⁠
• MAFFT⁠
• FastTree⁠
• ffdb⁠
• mpich⁠

Versions of software are available as environment variables and labels in the containers.

⁠Versioning

The container tags will correspond to a release of the pclust pipeline. They are intended to be paired so that the correct commands are used etc. It is possible that two docker builds with different tags will be identical because the pipeline has changed but the software dependencies haven't.

⁠Optimisation

Because MMSeqs2 requires a processor capable of using at least SSE4 instructions, this pipeline also has that minimum requirement. If you're unsure about your processors capability, on linux you can run the command grep "sse\|avx" /proc/cpuinfo to get a list of your CPUs capabilities.

We've done our best to dynamically handle different vectorisation instruction sets in the image. There should be at least a version that works with SSE and one that works with AVX2, and the correct version should be selected depending on your own processor.

If you really want to squeeze every bit of performance out of whatever you have, you might need to compile the software yourself using the -march=native gcc compiler options (or equivalent for your compiler).

Both MMseqs and HHsuite are compiled with MPI support (mpich).

⁠Build system

Because there are a few different bits of software, the container is built locally and pushed. Dockerfiles and the Makefile that coordinates building is available at github.com/darcyabjones/pclust/tree/master/containers⁠.

If you're uncomfortable about running unverified containers you might like to build it yourself.

There is also a Singularity⁠ version of the container available at cloud.sylabs.io/library/_container/5d71f338cb093ee1142b8791⁠ which should be signed with a pgp key and has fewer security risks associated (no sudo).