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Last pushed: a year ago
Short Description
Dockerized Discovar De Novo
Full Description

discovarDeNovo

Dockerized DISCOVAR de novo

what

This is a repo containing a Dockerfile for creating an ubuntu image with the de novo genome assembler DISCOVAR de novo (DDN) which was created by the BROAD Institute. This Dockerfile can be built by users but is also used to create an automatically-built image on Docker hub here.

usage

In order to run DISCOVAR de novo using the image on Docker hub built from this Dockerfile, enter the directory containing your read files and run the docker image as follows, entering the DISCOVAR de novo command-line arguments after vera/discovarDeNovo (in this example, assumes your input reads are all files ending in fastq.gz):

docker run -d --name ddn1 -v $(pwd):/ddn vera/discovardenovo READS=*fastq.gz NUM_THREADS=24 OUT_DIR=ddn

The docker container running DDN will output files in a directory ddn in the current directory. You can monitor the run by examining the log files generated by DDN, and by using the docker logs command with the name of the container specified with --name when creating the container:

docker logs -f ddn1
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Owner
vera
Source Repository