nmdp-bioinformatics/service-ars

Name: service-ars

Owner: NMDP/Be The Match Bioinformatics Research

Description: ARS reduction service

Created: 2015-08-17 20:52:33.0

Updated: 2016-08-11 21:01:13.0

Pushed: 2016-08-28 22:46:09.0

Homepage: null

Size: 1126

Language: Perl

GitHub Committers

User	Most Recent Commit	# Commits

Other Committers

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README

service-ars

RESTful Service for Antigen Recognition Site Reduction

Build

Docker Image

Further documentation is available at service-ars.readthedocs.io

Using service-ars

# Do ARS reduction on a typing #
curl http://localhost:3000/api/v1/redux?typing=A*01:01?dbversion=3.20

# Do ARS reduction on multiple subjects # 
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 all the ARS data #
curl http://localhost:3000/api/v1/ars

# Get all the ARS data for IMGTDB 3.20.0 #
curl http://localhost:3000/api/v1/ars?dbversion=3.20.0

Tools

ex. config.json

arsFile":"hla_nom_g.txt",
dbversion":"3.20.0",
arsUrl":"http://localhost:3000",
macUrl":"http://devgenomicservices1.nmdp.org/mac",
arsType":"g"

Java

typing-resolution

ments:
a, --about  display about message [optional]
h, --help  display help message [optional]
i, --input-file [class java.io.File]  input file, default stdin [optional]
j, --json-file [class java.io.File]  json configuration file [required]
x, --xml  print output as xml [optional]
s, --json  print output as json [optional]
c, --csv  print output as csv [optional]

ash
typing-resolution -j config.json -x < inputFile.xml > outputFile.xml
typing-resolution -j config.json -x -i inputFile.xml > outputFile.xml
typing-resolution -j config.json -c -i inputFile.xml > outputFile.csv
typing-resolution -j config.json -s -i inputFile.xml > outputFile.json

Perl

s-resolution [--config] [--verbos] [--help]
-c/--config
-v/--verbose
-h/--help

ash
resolution -c config.json < testInput.csv > testOutput.csv

Installing

ild.sh

Required Software

• JDK 1.7 or later, http://openjdk.java.net
• Apache Maven 3.2.5 or later, http://maven.apache.org
• Git, http://git.org
• perl 5.18 or later, http://perl.org

Perl Modules

• YAML
• Plack
• Plack::Handler::Starman
• Template
• JSON
• Getopt::Long
• LWP::UserAgent
• Test::More Dancer

Related Pages

• docker-ars
• dockerhub