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Docker containers for Sequana

We do not provide Docker containers anymore. However, since sequana is posted on bioconda, one can get some Dokcer containers. For example version 0.4.1 is available as explained here below. For full list please checkout https://quay.io/repository/biocontainers/sequana

Example: sequana_coverage

To pull a Sequana container (here version 0.4.1), use this type of command:

docker pull quay.io/biocontainers/sequana:0.4.1--py35_0

Checkout the quay.io website. After pulling the image above, you can use it as follows:

docker run -v $PWD:/home/default -it quay.io/biocontainers/sequana:0.4.1--py35_0

Warning

once in the docker shell, go to /home/default. Here, this directory is linked to your real directory where you type "docker run..." so what you modify here is directly reflected in your directory !

Assuming you have a BED file JB409847 in your directory, otherwise uncomment the commented line here below:

cd /home/default
export MPLBACKEND="agg"
# wget https://tinyurl.com/y9j69t3k -O JB409847.bed
sequana_coverage --input JB409847.bed
exit

Back on your local directory, you should now see a ./report directory with the results of the analysis.