A docker image containing the following algorithms fully configured:
First you need to install Docker on your computer. You can find all the details here.
Then, to get our docker image, you need to type:
docker pull fjossinet/rnaseq
In general, these algorithms need input files. Consequently, you have to mount the file system of your computer (the host) in the Docker container (the guest). This is done with the -v option.
SAMtools algorithm:
docker run -v /Users/fjossinet/my_files:/data fjossinet/rnaseq samtools view -c /data/my_file.bam