HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
Building the Docker Container
To build the Docker container:
$ docker build -t dockerbiotools/hmmer .
To list the programs available with HMMER:
$ docker run --rm dockerbiotools/hmmer ls
To run a program:
$ sudo docker run --rm --privileged -v /host/path:/data dockerbiotools/hmmer hmmer-program args
Since Docker containers have isolated file systems and changes to those filesystem do not persist between runs, you will need to mount a local directory inside the Docker container. To do so, replace
/host/path with a local directory in the above command. Use the path
/data in script arguments.
You can run
hmmsearch like so:
$ sudo docker run --rm --privileged -v ~/Data/hmmer:/data dockerbiotools/hmmer python hmmsearch --tblout /data/hits.txt /data/gpcrs.hmm /data/anopheles.fasta