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
#!/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" |
# 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"]} |
<?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> |
@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. |
@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 |
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
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.
The following Bash shell script will be used to add a port to the SSH service.
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 |
This document is an overview of how concepts from TES map to concepts in AWS Batch.
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
#!/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 |