zlemmon/rnaseq repository overview

⁠RNAseq snakemake pipeline tool container

Pre-installed tools for rnaseq on ubuntu core with miniconda3. Produced by ZHL.

Please remember that Docker containers do NOT save files unless you copy them out of the container and/or mount the volumes (-v option) as part of the set up. For instance you could mount a volume in the container locally to get results out, or if the results are spit to STDOUT then just capture with typical redirection to file.

⁠Instructions

Pull container docker pull zlemmon/rnaseq:latest

Run container various ways:

For interactive session:

docker run --rm -it zlemmon/rnaseq:latest

If awscli will be used from within container you need to include your credentials in the docker run command. Should be mounted in /home/docker/.aws. The following starts an interactive shell with your credentials mirrored over so for instance aws s3 ls will work.

docker run --rm -v ~/.aws:/home/docker/.aws -it zlemmon/rnaseq:latest

Run commands through container by simply following the docker run with what you'd like to do

Examples: -docker run --rm -v ~/.aws:/home/docker/.aws -it zlemmon/rnaseq:latest aws s3 cp SOURCE DEST -docker run --rm -v /home/docker/data:$HOME/data -t zlemmon/rnaseq:latest samtools view A.BAM > /home/docker/data/A.SAM

⁠installed tools

-cutadapt -fastqc -hisat2 -samtools -subread -trim-galore -trimmomatic