Run docker phenoxome

run-phenoxome.md

Data download; put data in /absolute/local/data/, called YOUR_DIR below

• Make a directory to hold data (/absolute/local/data/).
• Make these folders under your data dir: phenoxome_data/
• Put data in {YOUR_DIR}/phenoxome_data/
  • human_g1k_v37.fasta
  • HGMD.vcf.gz and HGMD.vcf.gz.tbi (rename HGMD file in vcfanno toml file)
  • gnomad.exomes.r2.0.1.sites.vcf.gz and gnomad.exomes.r2.0.1.sites.vcf.gz.tbi

Start the phenoxome container with a mount to your local data.

docker run --detach-keys="ctrl-@" --user $(id -u) -it -v /absolute/local/data/:/mnt/isilon/ samesense/phenoxome /bin/bash

Enter the container as root, and start mysql:

docker ps
# find CONTAINER_ID from `docker ps` result
docker exec -it --user root --detach-keys="ctrl-@" {CONTAINER_ID} bash run

# inside container, start mysql
/etc/init.d/mysql start

Run phenoxome inside the container (non-root user)

java -Xmx4g -jar /opt/conda/envs/phen/bin/Phenoxome_standalone_container.jar /mnt/isilon/your.vcf /mnt/islon/your_hpo.txt DGD_sample 0.002 /opt/snpeff_vcfanno.sh /opt/conda/envs/phen/bin/vt /mnt/isilon/cbmi/variome/perry/projects/sarmadi/phenoxome_data/human_g1k_v37.fasta /opt/conda/envs/phen/share/snpeff-4.2-0/snpEff
.jar /opt/conda/envs/phen/bin/vcfanno /opt/vcfanno_phenoxome.toml

Where did you get the files that you place in phenoxome_data? Thanks, Paul

Does this container even contain the necessary jar file to run?

docker run -it samesense/phenoxome ls /opt/conda/envs/phen/bin/Phenoxome_standalone_container.jar

Gives the result:

ls: cannot access '/opt/conda/envs/phen/bin/Phenoxome_standalone_container.jar': No such file or directory