ldipotetjob / poc-aws-s3

README

This repository is a proof of concept about the implementation of some bioinformatic tools in docker.

Setting up

• AWS
• Docker
  • docker build -t image_name:tag .
  • docker run --name container_name --rm -ti image_name:tag tool_to_execute
• BioInformatic tools scripts ./src/spades.sh ./src/sickle.sh ./src/fastqc.sh

Calling tools(tool_to_execute)

(tag:test) two choices

1. sickle: ./src/sickle.sh /data/xxxx_1.fastq.gz /data/xxxx_2.fastq.gz
2. sickle + spades + fasqc: ./src/executor.sh

example

1. $ docker run --name genx --rm scadip/aws-batch-poc:test ./src/sickle.sh /data/xxxx_1.fastq.gz /data/xxxx_2.fastq.gz
2. $ docker run --name genx --rm scadip/aws-batch-poc:test ./src/executor.sh

Contact us

Scadip

ref.: install jupyter notebook on docker linux: