Login worker

#!/bin/bash

shopt -s expand_aliases

alias ~=”:«’~bash’”

:«’~~~bash’

Usage

./loginWorker.md

Introduction

Login to a temporary container of the image ghcr.io/ljw20180420/celery_worker. The container will be remove automatically after exiting. This script accept a dataPath parameter (default to ./data). The dataPath contain the input .(fastq|fq)[.(gz|zip)] files. It maps to /app/data as a volume. The dataPath may optionally contain the genome and the corresponding bowtie2 index. These are necessary for using the automatic reference extraction of the in-house sx module. The WorkingDir of ghcr.io/ljw20180420/celery_worker is /app.

Source

read -ep "please input the full path of directory containing .(fq|fastq)[.(zip|gz)] inputs and other necessary data:" dataPath
if [ -z $dataPath ]
then
    echo "No dataPath is specified. Use default ./data as dataPath." >&2
    dataPath='./data'
fi
docker run -it --rm \
-v "./test:/app/test" \
-v "$dataPath:/app/data" \
ghcr.io/ljw20180420/celery_worker /bin/bash

alias ~~~=":" # This suppresses a warning and is not part of source.