README for FimTyper tool

This repository contains docker file to run FimTyper with linux docker image.

Building FimTyper docker image

• move to FimTyper root directory(Dockerfile)
• docker build -t genomixcloud/fimtyper .

Testing fimtyper installation:

 docker run --name fimtyper --rm -ti genomixcloud/fimtyper \
 perl /usr/local/fimtyper/fimtyper.pl

Running from local with test data

ref: https://bitbucket.org/genomicepidemiology/fimtyper/src/master/README.md#usage

 docker run --name fimtyper --rm -ti genomixcloud/fimtyper \
 perl /usr/local/fimtyper/fimtyper.pl \
 -d /usr/local/fimtyper/fimtyper_db -i \
 /usr/local/fimtyper/test.fsa -k 95.00 -l 0.60

Design recommendations for implement and running FimTyper on AWS:

AWS S3

Mandatory

In Dockerfile file:

Under comment # install awscli add the following code:

RUN wget -P /usr/src/ https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip && \
unzip -d /usr/src/  /usr/src/awscli-exe-linux-x86_64.zip && \
rm /usr/src/awscli-exe-linux-x86_64.zip && \
/usr/src/aws/install && \
mkdir /src && mkdir /conf

Other considerations:

1. The image contains 2 directories (/src, /conf).
2. The /src/fimtyper.sh can include a call to FimTyper tool and in and out directories linked with AWS S3. The previous link can be configured in /conf folder
3. With the previous configuration you can try run the commands below.

docker build -t ${your_own_workspace}/fimtyper .

docker run --name fimtyper --rm -ti \
-e AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
-e AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
--mount src="$(pwd)",target=/data,type=bind \
${your_own_workspace}/fimtyper /src/fimtyper.sh s3://fas_file_uri

AWS S3 + AWS ECS + AWS BATCH

1. In the src directory create /src/fimtyper.sh, it must include a call to the /usr/local/fimtyper/fimtyper.pl tool and the input directory linked with AWS S3. You can place the S3 configuration and the parameters for the FimTyper tool in /conf folder.
2. Push the image to your AWS Account (AWS ECR)
3. Create an AWS BATCH job that points to the FimTyper image, previously uploaded in AWS ECR.

In this implementation, we just pointed to the core aspect. Be aware that a first glance, you will need to configure AWS services like AWS Networking, AWS IAM, AWS S3, AWS Batch

ref:

• FimTyper main documentation