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

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• 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:

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• 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