dockerbiotools/hmmer repository overview

⁠HMMER

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 .

⁠Running 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