guigolab/ggsashimi repository overview

⁠ggsashimi docker image

To execute ggsashimi with docker:

docker run guigolab/ggsashimi --help

Because the image is used in a docker container which has its own file system, to use the program with local files, a host data volume needs to be mounted.

As an example, you can run this command from the main repository folder:

docker run -w $PWD -v $PWD:$PWD guigolab/ggsashimi -b examples/input_bams.tsv -c chr10:27040584-27048100

The '-w' option sets the working directory inside the container to the current directory. The '-v' option mounts the current working directory and all child folders inside the container to the same path (host_path:container_path).

If your files are in another folder, for example the annotation file is stored in a different folder then the one containing the bam file, you can mount extra folders like this:

f="$DIR/annotation.gtf"
docker run -w $PWD -v $PWD:$PWD -v $DIR:$DIR guigolab/ggsashimi -b examples/input_bams.tsv -c chr10:27040584-27048100 -g $f

You can even mount a single file:

docker run -w $PWD -v $PWD:$PWD -v $f:$f guigolab/ggsashimi -b examples/input_bams.tsv -c chr10:27040584-27048100 -g $f