Using docker image¶
Make sure you have Docker Engine installed. Note that you’ll need root access for the installation.
(recommended) If you plan to utilize GPU install Nvidia Container Toolkit
Pull docker image
docker pull quay.io/vitkl/cell2location
Run docker container with GPU support
docker run -i --rm -p 8848:8888 --gpus all quay.io/vitkl/cell2location:latest
Docker is an isolated execution environment, so by default it doesn’t have access to your local files. You need to mount your local directory to your docker container:
docker run -v /host/directory:/container/directory -i --rm -p 8848:8888 --gpus all quay.io/vitkl/cell2location:latest
For running without GPU support use
docker run -i --rm -p 8848:8888 quay.io/vitkl/cell2location:latest
Go to http://127.0.0.1:8848/?token= and log in using
cell2loc
token
Using singularity image¶
Singularity environments are used in the compute cluster environments (check with your local IT if Singularity is provided on your cluster). Follow the steps here to use it on your system, assuming that you need to use the GPU:
Download the container from our data portal:
wget https://cell2location.cog.sanger.ac.uk/singularity/cell2location-v0.06-alpha.sif
Submit a cluster job (LSF system) with GPU requested and start jupyter a notebook within a container (
--nv
option needed to use GPU):
bsub -q gpu_queue_name -M60000 \
-R"select[mem>60000] rusage[mem=60000, ngpus_physical=1.00] span[hosts=1]" \
-gpu "mode=shared:j_exclusive=yes" -Is \
/bin/singularity exec \
--no-home \
--nv \
-B /nfs/working_directory:/working_directory \
path/to/cell2location-v0.06-alpha.sif \
/bin/bash -c "cd /working_directory && HOME=$(mktemp -d) jupyter notebook --notebook-dir=/working_directory --NotebookApp.token='cell2loc' --ip=0.0.0.0 --port=1237 --no-browser --allow-root"
Replace 1) the path to /bin/singularity
with the one availlable on your system; 2) the path to /nfs/working_directory
to the directory which you need to work with (mount to the environment, /nfs/working_directory:/working_directory
); 3) path to the singularity image downloaded in step 1 (path/to/cell2location-v0.06-alpha.sif
).
Take a note of the cluster node name
node-name
that the job started on. Go to http://node-name:1237/?token= and log in usingcell2loc
token