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Other software

In rare cases, some software tools are not readily available through conda or biocontainers. Below are some guides on how to run some them.

ARB

ARB version 6.0 can be installed through conda from the bioconda channel, however it is not maintained anymore, and the latest version 7.0 is not available. To run version 7.0 on BioCloud, you need to run a wrapper script that runs ARB 7.0 from a custom container image. You can do that in a virtual desktop started from the web portal, or through an interactive shell session using salloc or srun. The convenient thing about the latter is that windows will show up on your own computer, but everything is running inside a SLURM job on a BioCloud compute node:

srun --cpus-per-task 2 --mem 4G --time 0-3:00:00 --x11 bash /shared_software/biocloud-software/arb/run.sh

As mentioned in the job submission guide ensure that you have X11 forwarding enabled for your SSH connection if you want to run things through SSH using salloc or srun.

To run things in a virtual desktop, simply open a terminal and run bash /software/biocloud-software/arb/run.sh.

CLC

CLC is licensed software tied to specific machines and is only available through a virtual desktop on nodes with the clc node feature listed. So ensure that you write --constraint clc in the "Additional job options" field. You can then find CLC in the menus.

AlphaFold

AlphaFold is quite complex to install and run. It runs through containers, but through a python wrapper script. Copy the SLURM sbatch script from /shared_software/biocloud-software/alphafold_singularity/sbatch_example.sh and adjust to suit your needs. AlphaFold benefits from GPU-accelerated servers, but can also run on regular CPUs. So submit to the appropriate partition.

To make folders available inside the container you need to bind/mount them, as described here.

usearch11

usearch11 is made available on all servers by simply running usearch11 or usearch.