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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
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