hurwitzlab/docker-virsorter

Name: docker-virsorter

Owner: Hurwitz Lab

Description: Docker for Virsorter

Created: 2015-09-01 22:18:23.0

Updated: 2017-10-13 18:39:50.0

Pushed: 2017-10-13 18:39:49.0

Homepage: null

Size: 42

Language: Shell

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README

Docker Virsorter

Docker for Virsorter

Dependencies

Install the following into a “bin” directory:

• HMMER (http://hmmer.janelia.org/)
• MCL (http://micans.org/mcl/)
• Metagene Annotator (http://metagene.nig.ac.jp/metagene/download_mga.html)
• MUSCLE (http://www.drive5.com/muscle/)
• BLAST (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/, not BLAST+)

Data Container

The 12G of dependent data exists as a separate data container called “virsorter-data.”

This is the Dockerfile for that:

FROM perl:latest

MAINTAINER Ken Youens-Clark <kyclark@email.arizona.edu>

COPY Generic_ref_file.refs /data/

COPY PFAM_27 /data/PFAM_27

COPY Phage_gene_catalog /data/Phage_gene_catalog

COPY Phage_gene_catalog_plus_viromes /data/Phage_gene_catalog_plus_viromes

COPY SUP05_SAGs_with_viruses.fna /data/

VOLUME ["/data"]

Do a “docker build -t kyclark/virsorter-data .” with that, then:

$ docker create --name virsorter-data kyclark/virsorter-data /bin/true

Build

$ docker build -t kyclark/virsorter .

Run

A sample “run” command to use the current working directory for input/output:

$ docker run --rm --volumes-from virsorter-data -v $(pwd):/de-app-work \
-w /de-app-work kyclark/virsorter --fasta Mic_1.fna

Authors

Simon Roux roux.8@osu.edu is the author of Virsorter

Ken Youens-Clark kyclark@email.arizona.edu packaged this for Docker/iPlant.