This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
See which versions are available:
$ module avail srst2
Load one version into your environment and run it:
$ module load srst2/git-73f885f5 $ srst2 --version
Note: Please use the ''--threads'' option to tell panaroo how many CPU cores/threads it should use. This number should match the number of CPUs you requested in your SLURM batch allocation.
Notes from the sysadmin during installation:
$ module load python/2.7 $ sudo mkdir -p /export/apps/srst2/git-73f885f5 $ sudo chown aorth:aorth /export/apps/srst2/git-73f885f5 $ virtualenv /export/apps/srst2/git-73f885f5/venv $ source /export/apps/srst2/git-73f885f5/venv/bin/activate $ pip install scipy $ pip install git+https://github.com/katholt/srst2 $ sudo chown -R root:root /export/apps/srst2/git-73f885f5
See also, the bioconda recipe for srst2.