docker-Bio-STR-exSTRa

Docker build for the Perl module Bio::STR::exSTRa.

Allows the use of Docker to run the exSTRa_score.pl Perl script without having to worry about dependencies.

Retrieving the repository:

docker pull ricktankard/bio-str-exstra:latest

The Docker container provides 'exSTRa_score.pl' as an executable.

For example, if using the example script: https://github.com/bahlolab/Bio-STR-exSTRa/blob/master/examples/run_strexpansion_score.sh

In the final command:

# Please set the correct path for the exSTRa_score.pl script
perl "$exstra_score" \
    "$reference" \
    "$repeat_database" \
    $bam_glob \
    > "$output"

replace perl "$exstra_score" with:

docker run <mount command> ricktankard/bio-str-exstra:latest exSTRa_score.pl

You will need to appropriately set up mounts for your data, replacing <mount command> as for Docker in general.

An example of a full command with all input files in a directory named 'inputs', that writes to a file output/exSTRa_scores.txt is:

docker run --mount type=bind,source="$(pwd)"/input,target=/input \
    ricktankard/bio-str-exstra:latest \
    exSTRa_score.pl \
    /input/path/to/hg19.fa \
    /input/path/to/repeat_expansion_disorders.txt \
    /input/path/to/bams/*.bam \
    > output/exSTRa_scores.txt

Dockerfile

The Dockerfile for this container can be found in https://github.com/trickytank/docker-Bio-STR-exSTRa.