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braker

Docker container for running braker gene finder

https://github.com/blaxterlab/braker-docker

To use this docker you should

  1. checkout this repo:
git clone https://github.com/blaxterlab/braker-docker.git
cd braker-docker
  1. Download your OWN copy of the genemark executables and key which you can get from http://exon.gatech.edu/GeneMark/license_download.cgi (pick the GeneMark-ES / ET v.4.33 LINUX 64 option for this docker) and save gm_key_64.gz and gm_et_linux_64.tar.gz in the braker-docker folder

  2. Run docker build:

docker build -t braker .
  1. Go to the folder where you have the aligned.bam and genome.fasta files (or replace pwd with the absolute path of that folder) and run braker:
docker run --rm \
  -u $UID:$GROUPS \
  -v `pwd`:/data \
  braker \
  braker.pl --species=YOURSPECIESNAME --UTR=on --cores=8 \
  --genome=/data/genome.fasta \
  --bam=/data/aligned.bam
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blaxterlab

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