Docker image based on Ubuntu Focal with bam-readcount v1.0.0 built
and installed. Note that this does not build from master, but the
v1.0.0 tag. Edit the Dockerfile to use master or a different branch
or tag.
This Dockerfile has a corresponding build in Dockerhub https://hub.docker.com/r/mgibio/bam-readcount
docker pull mgibio/bam-readcount
The bam-readcount binary is installed as
/usr/bin/bam-readcount
https://github.com/genome/bam-readcount
bam-readcount source and documentation
https://docs.docker.com/
Docker documentation
The Dockerfile sets
ENTRYPOINT ["/usr/bin/bam-readcount"]
so the container can be run as an executable.
For example, to run bam-readcount on a FASTA reference REFERENCE and
BAM file BAMFILE in the current working directory, you can do
# --rm
# Remove container when done
# -v $(pwd):$(pwd)
# Maps the current working directory to the same path inside the container
# -w $(pwd)
# Sets the working directory to the current working directory inside
# the container
docker run --rm -v $(pwd):$(pwd) -w $(pwd) mgibio/bam-readcount -f REFERENCE BAMFILE
The ENTRYPOINT can be overridden for interactive use.
For example, to run bam-readcount on test data included in the container,
do
# --rm
# Remove container when done
# -it
# Docker interactive flags
# --entrypoint /bin/bash
# Set the Bash shell as the entrypoint
docker run --rm -it --entrypoint /bin/bash mgibio/bam-readcount
The container will present an interactive prompt, and the working directory
will be /opt/bam-readcount. There is a directory test-data there, and
bam-readcount can be run on this data with
# -w1
# The test BAM does not have the SM tag; -w1 will report warnings
# only once to avoid a warning for each read
root@3a0a8df8b278:/opt/bam-readcount# bam-readcount -w1 -f test-data/ref.fa test-data/test.bam
To make your own data available for interactive use within the container,
use the Docker -v and -w flags to map your local directories and
set a working directory, for example to use the current working local
directory
docker run --rm -it -v $(pwd):$(pwd) -w $(pwd) --entrypoint /bin/bash mgibio/bam-readcount