Skip to content

Latest commit

 

History

History
181 lines (117 loc) · 5.46 KB

README.md

File metadata and controls

181 lines (117 loc) · 5.46 KB
Raw

sequenceserver-scale-docker

docker container for (sequenceserver-scale)[https://github.com/zhxu73/sequenceserver-scale]

This repo include 4 docker containers:

- Web/Master Worker
iRODS zhxu73/sequenceserver-scale:latest zhxu73/sequenceserver-scale-worker:latest
No iRODS zhxu73/sequenceserver-scale:no-irods zhxu73/sequenceserver-scale-worker:no-irods

There are 2 ways to make the database available to sequenceserver: one is with iRODS -e IRODS_SYNC_PATH=/iplant/home/shared/iplantcollaborative/example_data/GEA_Blast_dbs the other is by bind mount local directory.

They can be used interchangably, as even with non-docker (native) deployment, as long as the database path inside docker are the same, and BLAST binary installed in $PATH:

e.g. Use iRODS master docker with a No-iRODS worker

Expand
  • Master
docker run --rm -ti -p 80:3000 -p 9123:9123 -e PROJECT_NAME=starBLAST -e WORKQUEUE_PASSWORD= -e BLAST_NUM_THREADS=4 -e SEQSERVER_DB_PATH=/home/zhxu73/db zhxu73/sequenceserver-scale
  • Worker
docker run --rm -ti -p 80:3000 -p 9123:9123 -e PROJECT_NAME=starBLAST -e WORKQUEUE_PASSWORD= -e BLAST_NUM_THREADS=4 -e SEQSERVER_DB_PATH=/home/zhxu73/db -v $HOME/blastdb:/home/zhxu73/db zhxu73/sequenceserver-scale:no-irods

e.g. Use iRODS master docker with native work_queue_factory

Expand
  • Master
docker run --rm -ti -p 80:3000 -p 9123:9123 -e PROJECT_NAME=starBLAST -e WORKQUEUE_PASSWORD= -e BLAST_NUM_THREADS=4 -e SEQSERVER_DB_PATH=/home/zhxu73/db zhxu73/sequenceserver-scale
  • Worker
iinit
mkdir -p /home/zhxu73/db
irsync -rKv i:/iplant/home/shared/iplantcollaborative/example_data/GEA_Blast_dbs /home/zhxu73/db
work_queue_factory -T local -M starBLAST -w 1 --cores=4

Web/Master docker image

https://hub.docker.com/repository/docker/zhxu73/sequenceserver-scale

Available Environment Variable:

Expand

  • PROJECT_NAME

    This option utilize the catalog server

    Default to empty (not set)

  • WORKQUEUE_PASSWORD

    Password between master and worker

    Use -e WORKQUEUE_PASSWORD= to set to empty (no password)

  • BLAST_NUM_THREADS

    Number of threads the blast program will be running with

    Should be consistent with the value set for worker container

    Default to 4

  • SEQSERVER_DB_PATH

    Path of database inside the container, should be consistent between master and worker

    Default to /var/www/sequenceserver/db

  • IRODS_SYNC_PATH

    iRODS (tag latest) container only

    The iRODS path to download the database from.

    Default to /iplant/home/shared/iplantcollaborative/example_data/GEA_Blast_dbs

Example Usage:

With iRODS

docker run --rm -ti -p 80:3000 -p 9123:9123 -e PROJECT_NAME=starBLAST -e WORKQUEUE_PASSWORD= -e BLAST_NUM_THREADS=4 zhxu73/sequenceserver-scale

docker run --rm -ti -p 80:3000 -p 9123:9123 -e PROJECT_NAME=starBLAST -e WORKQUEUE_PASSWORD= -e BLAST_NUM_THREADS=4 -e SEQSERVER_DB_PATH=/home/zhxu73/db zhxu73/sequenceserver-scale

Without iRODS

docker run --rm -ti -p 80:3000 -p 9123:9123 -e PROJECT_NAME=starBLAST -e WORKQUEUE_PASSWORD= -e BLAST_NUM_THREADS=4 -v /local_db_path:/var/www/sequenceserver/db zhxu73/sequenceserver-scale:no-irods

docker run --rm -ti -p 80:3000 -p 9123:9123 -e PROJECT_NAME=starBLAST -e WORKQUEUE_PASSWORD= -e BLAST_NUM_THREADS=4 -e SEQSERVER_DB_PATH=/home/zhxu73/db -v $HOME/blastdb:/home/zhxu73/db zhxu73/sequenceserver-scale:no-irods

Worker docker image

https://hub.docker.com/repository/docker/zhxu73/sequenceserver-scale-worker

Available Environment Variable:

Expand

  • PROJECT_NAME

    Default to empty (not set), if set (not empty), then MASTER_IP will be ignored

  • MASTER_IP

    IP address of the master

    Default to 127.0.0.1 (localhost)

  • WORKQUEUE_PASSWORD

    Password between master and worker

  • BLAST_NUM_THREADS

    Number of threads the blast program will be running with

    Default to 4

  • NUM_WORKER

    Number of work_queue_worker to be spawned by the work_queue_factory

    NUM_WORKER * BLAST_NUM_THREADS should not exceed the number of CPU/cores the instance (that runs the worker container) have

    Default to 1

  • SEQSERVER_DB_PATH

    iRODS (tag latest) container only

    Path of database inside the container, should be consistent between master and worker

    Default to /var/www/sequenceserver/db

  • IRODS_SYNC_PATH

    iRODS (tag latest) container only

    The iRODS path to download the database from.

    Default to /iplant/home/shared/iplantcollaborative/example_data/GEA_Blast_dbs

Example Usage:

With iRODS

docker run --rm -ti --net=host -e PROJECT_NAME=starBLAST -e WORKQUEUE_PASSWORD= -e BLAST_NUM_THREADS=4 -e NUM_WORKER=2 zhxu73/sequenceserver-scale-worker

docker run --rm -ti --net=host -e PROJECT_NAME=starBLAST -e WORKQUEUE_PASSWORD= -e BLAST_NUM_THREADS=4 -e NUM_WORKER=2 -e SEQSERVER_DB_PATH=/home/zhxu73/db zhxu73/sequenceserver-scale-worker

Without iRODS

docker run --rm -ti --net=host -e PROJECT_NAME=starBLAST -e WORKQUEUE_PASSWORD= -e BLAST_NUM_THREADS=4 -e NUM_WORKER=2 -v /local_db_path:/var/www/sequenceserver/db zhxu73/sequenceserver-scale-worker:no-irods