service-ars

Getting started

Overview

Antigen Recognition Site

ARS Groups

ARS Reduction

Service UI

Options

--hml
  • HML file
  • Required parameter
--output
  • Output directory
  • Required parameter
--imgtdir
  • Location of where the BLAST IMGT database is located
  • Default location is /opt/html on the docker container
--imgt
  • IMGT database version
  • Default is 3200
--report
  • Binary flag for generating HTML validation report
  • default is 1

Advanced options

--hml
  • HML file
  • Required parameter
--output
  • Output directory
  • Required parameter
--imgtdir
  • Location of where the BLAST IMGT database is located
  • Default location is /opt/html on the docker container
--imgt
  • IMGT database version
  • Default is 3200
--report
  • Binary flag for generating HTML validation report
  • default is 1

Submit HML File

Service API

RESTful Interface

Parameters

  • IMGT/DB
  • Glstring
  • ARS Type
  • MAC Url
  • Expand Genotypes
  • Expand Genomic Typing

Convert HLA Typing

curl --header "Content-type: application/json" --request POST
        --data '{"arsFile":"hla_nom_g.txt","dbversion":"3.20.0","arsType":"G",
        "Subjects":[{"SubjectID":1,"typing":["A*01:01+A*01:02","B*08:01+B*07:02","C*07:01+C*07:01"]},
        {"SubjectID":1,"typing":["A*01:01+A*01:02","B*08:01+B*07:02","C*07:01+C*07:01"]}]}'
        http://localhost:3000/api/v1/reduxSubjects

Convert Subject Typing

curl --header "Content-type: application/json" --request POST
        --data '{"arsFile":"hla_nom_g.txt","dbversion":"3.20.0","arsType":"G",
        "Subjects":[{"SubjectID":1,"typing":["A*01:01+A*01:02","B*08:01+B*07:02","C*07:01+C*07:01"]},
        {"SubjectID":1,"typing":["A*01:01+A*01:02","B*08:01+B*07:02","C*07:01+C*07:01"]}]}'
        http://localhost:3000/api/v1/reduxSubjects

Get ARS Data

./nextflow run nmdp-bioinformatics/flow-blast-hml -with-docker \
        nmdpbioinformatics/docker-blast-hml \
        --hml test_file.hml --outdir /path/to/output/dir

Clients & Tools

Java

  • hml-typing-resolution *
--hml
  • HML file
  • Required parameter
--output
  • Output directory
  • Required parameter
--imgtdir
  • Location of where the BLAST IMGT database is located
  • Default location is /opt/html on the docker container
--imgt
  • IMGT database version
  • Default is 3200
--report
  • Binary flag for generating HTML validation report
  • default is 1

Perl

--hml
  • HML file
  • Required parameter
--output
  • Output directory
  • Required parameter
--imgtdir
  • Location of where the BLAST IMGT database is located
  • Default location is /opt/html on the docker container
--imgt
  • IMGT database version
  • Default is 3200
--report
  • Binary flag for generating HTML validation report
  • default is 1

Developers

Contributing

  1. Log into Github web interface with your username-nmdp account
  2. Browse to the repo at https://github.com/nmdp-bioinformatics/flow-blast-hml, hit the Fork button.
  3. Copy the clone URL from the Github web page for the fork (something like https://github.com/username-nmdp/pipeline.git)
  4. Clone the fork
git clone https://github.com/username-nmdp/flow-blast-hml.git
cd flow-blast-hml
  1. Add upstream as remote
git remote add upstream https://github.com/nmdp-bioinformatics/flow-blast-hml
  1. Pull and merge latest changes from upstream master to your local master branch
git checkout master
git pull upstream master
git push
  1. Create a new local feature branch
git checkout -b new-feature-branch
  1. Edit files locally
  2. Commit changes to local feature branch
git commit -m "made changes"
  1. Push changes from local feature branch to remote feature branch on your fork
git push origin new-feature-branch
  1. Browse to the Github web page for your fork repo (something like https://github.com/username-nmdp/flow-blast-hml) and hit the new pull request button.
  2. Edit the pull request description and hit create new pull request button.
  3. Other contributors will review the changes in the pull request.
  4. When the pull request looks good, it will be merged into the master branch.
  5. Hit the delete branch button to delete your remote feature branch (the commits have been merge upstream, so it is no longer necessary).
  6. Delete your local feature branch
git branch -d new-feature-branch

Installation

Docker