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
.