renseq

Renseq Pacbio pipeline

Apologies for the size of this image, but it installs the entire PACBio SMRT-Analysis suite which is quite big. And apparently, to run the CLI smrtpipe.py, the whole suite must be installed, including a mysqldb and a full web stack for a web GUI that is never used (read below if it is really needed). Anyway, most of the bulk seem to be folders mysteriously named "parameters" with a date. Gigs worth of parameters, why not?

Combining this docker image with the entrypoint from the following gist, one can run the fully functional web-interface of the PacBio assembly pipeline.

Usage

1. renseq pipeline:

put your files in a folder that will be mounted in the image as a volume e.g. data. Then:

docker run -ti -v data:/home/admin/data cyverseuk/renseq /home/admin/data/adapter.fasta /home/admin/data/file1.h5 /home/admin/data/file2.h5 etc...

2. web-interface for PacBio assembly pipeline:

run this docker exposing port, mounting volumes and providing alternative entrypoint: docker run -dit --entrypoint ./scripts/runWeb.sh --expose 8080 -p 8080:8080 --volume /data:/data --name pacbio-container pacbio semantics:

3. general docker tips:

• building this image: docker build -t pacbio .
• ports and volumes mapping semantics: --port outside_port:inside_port --volume outside_path:inside_path
• to access running web-interface in the browser go to: 0.0.0.0:outside_port or your_hostname:outside_port