nmdp-bioinformatics/netMHC-spark

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

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README

netMHC-spark

Command line tool for running netMHC with Apache Spark

Install

clone https://github.com/nmdp-bioinformatics/netMHC-spark
etMHC-spark
package

Useage

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)

Example

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

• JDK 1.8
• Apache Maven 3.2.5 or later
• Scala
• Apache Spark 2.1.0
• NetMHC

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