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final class MyTask extends AbstractTask
{
    private final CyNetworkView networkView;
    private final VisualStyle style;
    private boolean lockedNodeView = false;
    private boolean lockedEdgeView = false;

    @Override
    public void run(final TaskMonitor taskMonitor)
    {

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// Copyright 2016 DSP Synthesizers Sweden. 
// 
// Author: Jan Ostman 
// 
// This program is free software: you can redistribute it and/or modify 
// it under the terms of the GNU General Public License as published by 
// the Free Software Foundation, either version 3 of the License, or 
// (at your option) any later version. 
// This program is distributed in the hope that it will be useful, 
// but WITHOUT ANY WARRANTY; without even the implied warranty of 

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ADAM on AWS using CGCloud

Create an EC2 instance as a CGCloud gateway

Installing CGCloud on a Mac is a bit of trouble, so installing to a linux VM or an EC2 instance on AWS might be helpful. Our client chose the latter, installing to a t2.small instance that is available all the time.

$ ssh -A cgcloud.foo.com

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$ ./bin/adam-shell --driver-memory 14g
Using SPARK_SHELL=/usr/local/bin/spark-shell
2018-03-14 12:02:18 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
Spark context Web UI available at http://l0504206.nmdp.org:4040
Spark context available as 'sc' (master = local[*], app id = local-1521046943951).
Spark session available as 'spark'.
Welcome to
      ____              __

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scala> import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.rdd.ADAMContext._

scala> import org.bdgenomics.adam.models._
import org.bdgenomics.adam.models._

scala> val partitioned = sc.loadPartitionedParquetAlignments("small.partitioned.alignments.adam")
2018-03-26 16:04:58 WARN  ObjectStore:568 - Failed to get database global_temp, returning NoSuchObjectException
partitioned: org.bdgenomics.adam.rdd.read.AlignmentRecordRDD = DatasetBoundAlignmentRecordRDD with 2 reference sequences, 0 read groups, and 2 processing steps

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import org.bdgenomics.adam.models.{ RecordGroup, RecordGroupDictionary }
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.rdd.fragment.InterleavedFASTQInFormatter
import org.bdgenomics.adam.rdd.read.{ AlignmentRecordRDD, AnySAMOutFormatter }
import org.bdgenomics.adam.sql.{ AlignmentRecord => AlignmentRecordProduct }
import org.bdgenomics.formats.avro.AlignmentRecord

val reads = sc.loadPairedFastqAsFragments("sample_1.fq", "sample_2.fq")

implicit val tFormatter = InterleavedFASTQInFormatter

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#!/bin/bash

cannoli-submit \
    interleaveFastq \
    sample_1.fq \
    sample_2.fq \
    sample.ifq

cannoli-submit \
    bwa \

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[INFO] --- exec-maven-plugin:1.5.0:exec (doc-r) @ adam-r-spark2_2.11 ---

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.cannoli.Cannoli._

val reads = sc.loadPairedFastqAsFragments("sample_1.fq", "sample_2.fq")

val bwaArgs = new BwaArgs()
bwaArgs.sample = "sample"
bwaArgs.indexPath = "/data/hs38DH.fa"
bwaArgs.useDocker = true
//bwaArgs.useSingularity = true

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# Generated 2015-09-14 by http://www.gilesorr.com/Code/bpb/ ,
# The Bash Prompt Builder written by Giles Orr.

case ${TERM} in
  xterm*|rxvt*)
    TITLEBAR='\[\033]0;\u@\h:\w\007\]';;
  *)
    TITLEBAR='';;
esac;
# Elegant code courtesy of nitrous.io: