Installation

Note

The following instructions are for installing and running the service locally for development purposes. If you just want to run the service locally, then refer to the documentaiton on running the Docker image instead.

Software Requirements

Before installing the GFE service locally, you’ll need to install some required software. If you want to reproduce the GFE service locally, then installing the ngs-tools and annotation pipeline from the file available in the docker directory is the safest method.

• Git
• Perl
• Java
• Annotation Pipeline
• nextflow
• ngs-tools

Perl Packages

Tip

Some perl modules will fail to load if you don’t have certain software installed. Make sure you have libssl-dev installed otherwise Moose and Log4j will fail to properly install.

1. Clone the `github repository`_
2. Change into the *service-gfe-submission directory, with the Makefile.PL file.
3. Install cpanm and all the perl dependencies. curl -LO http://xrl.us/cpanm && perl cpanm --notest --installdeps .

ngs-tools

There are several ways that you can build the ngs-tools needed for running the GFE service. The easiest and safest way would be to install from the debian file located in the docker directory. Make sure to export the location the ngs-tools in your PATH environment variable.

Installing From Debian

If you’re not worried about the mechanics of the ngs-tools, then installing it from the debian file located in the docker directory is the best method. Don’t use this debian for the testing and development of the ngs-tools.

cd service-gfe-submission/docker
dpkg --install ngs-tools_1.9.deb

Building locally

If you want to make some modifications to the ngs-tools and test it locally with the GFE service, then this is the best option for you. If you think the changes you make should be part of the ngs code base, then make sure to make a pull request to the ngs master branch on github.

git clone https://github.com/nmdp-bioinformatics/ngs
cd ngs
mvn install

Annotation Pipeline

Currently the annotaion pipeline is not able to be built from the github page. Instead you can install it locally, by unzipping the tar file in the docker directory. We’re currently working on adding this to the ngs code base on github.

cd service-gfe-submission/docker
tar -xzf hap1.2.tar.gz
export PATH=$PATH:`pwd`

Installing service-gfe-submission

Note

This step will fail if you don’t have the required software listed above installed and listed in the PATH environment variable. Make sure to add the nextflow, anootation pipeline and the ngs-tools to your PATH environment variable.

1. Clone the github repository.
2. Change to the directory of the Makefile.PL.
3. Run make test and make install. perl Makefile.PL && make && make test && make install
4. Run the service locally. plackup bin/app.pl
5. Go to http://localhost:5000 for the GUI and access to the Swagger API.
6. Now test the service with curl.

curl --header "Content-type: application/json" --request POST \
--data '{"locus":"HLA-A","gfe":"HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-0"}' \
http://localhost:5000/sequence