# vireoSNP on Bianca

https://vireosnp.readthedocs.io/en/latest/install.html

Login on `transit.uppmax.uu.se` https://uppmax.github.io/UPPMAX-documentation/cluster_guides/transit/

## On transit

# Mount the wharf project folder in your home folder
mount_wharf sensXXXXXX

# Enter the wharf directory
cd sensXXXXXX

# pull pre-build container of the tool
singularity pull oras://community.wave.seqera.io/library/vireosnp:0.5.8--bcb737f6b5281b4f
chmod +x vireosnp_0.5.8--bcb737f6b5281b4f.sif

# test the container
./vireosnp:0.5.8--bcb737f6b5281b4f vireo

Welcome to vireoSNP v0.5.8!
use -h or --help for help on argument.

## On Bianca

# Go to you project folder
cd /proj/sensXXXXXX/USER

# bring (move) the container
# somewhere in the project from the wharf
# note the "." at the end
mv /proj/sensXXXXXX/nobackup/wharf/USER/USER-sensXXXXXX/vireosnp:0.5.8--bcb737f6b5281b4f .

# test
./vireosnp:0.5.8--bcb737f6b5281b4f vireo

Welcome to vireoSNP v0.5.8!
use -h or --help for help on argument.

## Building newer or diferent version of the tool
Visit https://seqera.io/containers/ (no account needed). Search for "vireosnp" and add the "bioconda" package, chose "Singularity" for the container, then push "Get Container". Wait to build, copy the link and follow the instructions above.

## Contacts:
- [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425)
- [UPPMAX](https://www.uu.se/en/centre/uppmax)
- [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ)

###### tags: `UPPMAX`,