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#!/bin/sh
cd /tmp
git clone https://github.com/mpitutorial/mpitutorial
cd mpitutorial/tutorials/mpi-hello-world/code
# grab the mpicc PATH locations
source /etc/profile.d/efa.sh
make all
cp mpi_hello_world /shared/mpi_hello_world

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Map of Task Execution Service (TES) to AWS

This document is an overview of how concepts from TES map to concepts in AWS Batch.

AWS Batch - Basic Concepts

AWS Batch ("Batch") has a few basic concepts that need to be understood before we can make a comparison to concepts in TES. Some relate directly to TES and others do not.

Job

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FROM rocker/r-base

RUN apt-get update
# install python tools
RUN apt-get install -y python-dev python-pip
# install AWS CLI
RUN pip install -U awscli

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Port 22 is BLOCKED! HALP!

The MCW auditorium wifi blocks the standard SSH network port, port 22. If you are to successfully connect to the EC2 instance from the MCW guest wifi, you will need to change the default port that the SSH service provides for connections. You will also need to allow network traffic to that port on the EC2 instance.

Step 1: the userdata script

The following Bash shell script will be used to add a port to the SSH service.

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Implementing a simple AWS Lambda function

In this lab, we will use the chalice Python serverless web application framework for AWS to create a REST API endpoint to reverse complement a DNA string using AWS Lambda and Amazon API Gateway.

# install chalice
$ pip install chalice

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@namespace("com.example")
/**
This is a comment for the whole protocol
*/

protocol Example {

/**

The comment applies to the `NoSpaces` record, but is not indented to the 

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@namespace("com.example")
/**
This is a comment for the whole protocol
*/
protocol Example {

  /**
  This is a paragraph with a 
  multi-line comment and 
  no spaces in between.

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<?xml version="1.0" encoding="ISO-8859-1"?>
<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
  <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="April_19_2013_sample002" version="1.1.0">
    <cvList count="2">
      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.30.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
      <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
    </cvList>
    <fileDescription>
      <fileContent>
      </fileContent>

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# request a single barcode as JSON
curl http://pidler.org/bc
curl http://pidler.org/bc.json
# => {"barcodes":["PA6A24"]}

# request 3 barcodes as JSON
curl http://pidler.org/bc?num=3
curl http://pidler.org/bc.json?num=3
# => {"barcodes":["P5D1EE","PB80CB","PC70A2"]}

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#!/usr/bin/env python
import boto
from os import environ

conn = boto.connect_ec2(environ["AWS_ACCESS_KEY_ID"],environ["AWS_SECRET_ACCESS_KEY"])
size = 100
#adjust to the same zone as StarCluster config
zone = "us-east-1a"
# Description: RUMv1.09, BWAv0.6.1, Bowtie2b5, Bowtie0.12.7, GATK1.4, samtools0.1.18
snapshot = "snap-aec239d5"