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Last pushed: 3 years ago
Short Description
A Dockerized version of Jared Simpson's SGA assembler,
Full Description

SGA-in-a-container, such that you can run the dockerized SGA much as you would run the local SGA executable.

Once built, you can invoke sga-docker as you would sga, eg:

docker run -v /path/to/local/data/data/:/data/ \
       sga-docker somatic-variant-filters --annotate-only --threads=2 \
       --tumor-bam=/data/tumor.bam --normal-bam=/data/normal.bam \
        --reference=/data/reference.fa /data/input.vcf

You can also invoke other sga scripts, such as sga-preqc-report:

docker run -v /path/of/sga/repo:/data/ \
       --entrypoint /src/sga-0.10.14/src/bin/ \
       sga-docker /data/src/examples/preqc/{bird,fish,human,oyster,snake,yeast}.preqc
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