docker_test

docker run --rm -it --ipc=host kishwars/helen:latest helen --help

/nvme_data/program_outputs/marginpolish/docker_test/

# download model
mkdir model_out

docker run \
-v "/nvme_data/program_outputs/marginpolish/docker_test/":"/data/" \
--rm -it --ipc=host --user=`id -u`:`id -g` \
kishwars/helen:latest \
helen download_models \
--output_dir /data/model_out/

docker run \
-v "/nvme_data/program_outputs/marginpolish/docker_test/":"/data/" \
--rm -it --ipc=host --user=`id -u`:`id -g` \
kishwars/helen:latest \
helen download_models \
--output_dir /data/model_out/

# run marginpolish
mkdir marginpolish_output

docker run \
-v "/nvme_data/program_outputs/marginpolish/docker_test/":"/data/" \
--rm -it --ipc=host --user=`id -u`:`id -g` \
kishwars/helen:latest \
marginpolish \
/data/Bacterial_reads_to_shasta_validate_StaphAur.bam \
/data/Bacterial_shasta_assembly_validate_StaphAur.fasta \
/data/model_out/MP_r941_guppy344_microbial.json  \
-t 38 \
-o /data/marginpolish_output/mp_images \
-f

# run HELEN
docker run \
-v "/nvme_data/program_outputs/marginpolish/docker_test/":"/data/" \
--rm -it --ipc=host --user=`id -u`:`id -g` \
kishwars/helen:latest \
helen polish \
--image_dir /data/marginpolish_output/ \
--model_path /data/model_out/HELEN_r941_guppy344_microbial.pkl \
--threads 38 \
--output_dir /data/helen_polished/


sudo apt-get install cmake wget bzip2 gcc-4.9 g++-4.9 zlib1g-dev libncurses5-dev python3-all-dev libhdf5-dev libatlas-base-dev libopenblas-base libopenblas-dev libbz2-dev liblzma-dev libffi-dev make python-virtualenv