Name: netMHC-spark

Owner: NMDP/Be The Match Bioinformatics Research

Description: netMHC Apache Spark CLI

Created: 2018-04-27 17:24:27.0

Updated: 2018-04-27 17:33:40.0

Pushed: 2018-04-27 17:28:11.0

Homepage: null

Size: 6

Language: Scala

GitHub Committers

UserMost Recent Commit# Commits

Other Committers

UserEmailMost Recent Commit# Commits



Command line tool for running netMHC with Apache Spark

clone https://github.com/nmdp-bioinformatics/netMHC-spark
hc-spark 1.0
e: spark-submit netmhc-spark-1.0-SNAPSHOT.jar [options]

, --input <value>    input is the input path
, --output <value>   output is the output path
, --alleles <value>  alleles is the list of HLA alleles to use
, --format <value>   format is the output format (default = parquet)
k-submit --master yarn --deploy-mode client \
target/netmhc-spark-1.0-SNAPSHOT.jar \
--input src/test/resources/test_peptides.pep \
--alleles src/test/resources/allele_list.txt \
--output peptide_binding
Required Software
NetMHC Reference

Massimo Andreatta, Morten Nielsen; Gapped sequence alignment using artificial neural networks: application to the MHC class I system, Bioinformatics, Volume 32, Issue 4, 15 February 2016, Pages 511?517, https://doi.org/10.1093/bioinformatics/btv639

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.