bmpvieira

Setting up Crashplan on FreeNAS Goals

Be able to backup from the FreeNAS box to offsite Crashplan Central. Allow incoming Crashplan backups from other devices. Install the CrashPlan plugin

Install the plugin into a jail: Click on Plugins, then the Available tab, the "crashplan" line and finally the Install button. Once the installation completes, on the left tree, expand Plugins and click on CrashPlan. Accept the Java EULA. Start the Crashplan plugin: Plugins->Installed and make sure the Crashplan plugin is in the "ON" position.

bmpvieira

# Setup R with LEA package (because it segfaults on OSX)
# http://membres-timc.imag.fr/Olivier.Francois/LEA/software.htm
# Run one by one the following commands 
brew install boot2docker docker
boot2docker init
boot2docker up
docker run -it -v ~/Downloads:/Downloads r-base
docker run -it r-base
install.packages("/Downloads/LEA_0.2.tar", repos = NULL, type = "source")

bmpvieira

#!/bin/bash
# Script to do one-line non-root install of Node.js on Ubuntu and OSX
# Depends on curl which sometimes isn't preinstalled on Ubuntu, so do:
# sudo apt-get install curl

INSTALL_PATH=$HOME/.nodejs

# Install n (Node.js versions manager)
cd /tmp
echo "Downloading n (Node.js versions manager)"

bmpvieira

How do you share and control/limit the data

How to limit the data:

• Masking the mendelian variants / restrict access to particular region of genome
• Aggregate the information to the population level
• Encrypt the data to still keep the patterns but not disclose the raw data

Issues:

• We might still get privacy concerning information from non-mendelian variants
• Population information might not be relevant for individuals (complex genes interactions, etc)
• Gets in the way of the research, and personalised medicine

bmpvieira

#!/usr/bin/env node
// Usage: ./filterRepeats.js <minimum> <file path>
// Example: ./filterRepeats.js 10 list.txt

var fs = require('fs')
var min = process.argv[2]
var listPath = process.argv[3]
var list = fs.readFileSync(listPath, 'utf8').split('\n')
var counter = {}
list.forEach(count)

bmpvieira

# Get Amazon AWS Command Line tool
brew install awscli

# Setup instance
aws configure # key, secret, eu-west-1, table
aws ec2 create-key-pair --key-name MyKeyPair --query 'KeyMaterial' --output text > MyKeyPair.pem
aws ec2 run-instances --image-id ami-f0b11187 --instance-type r3.4xlarge --region eu-west-1 --key-name MyKeyPair
aws ec2 describe-instances
aws ec2 authorize-security-group-ingress --group-id sg-86bfxxxx --protocol tcp --port 22 --cidr 0.0.0.0/0

bmpvieira

getCountryAgainstElevation <- function(genus) {
  table1 <- read.csv('http://bmpvieira.github.io/temp/alabamaants-myrmicinaepheidole_obscurithorax.csv', h=T)
  table2 <- read.csv('http://bmpvieira.github.io/temp/allantwebants-myrmicinaesolenopsis_invicta.csv', h=T)
  mergedtable <- # put code here to merge table1 and table2
  # Once you have the merged table:
  # 1. Subset the table to a new one with only the rows that match the Genus provided by the argument of the function
  # 2. Use the function table() to get Country against Elevation
  # e.g., something like table(countryColumn, elevationColumn)
  # 3. return the resulting table
  # The output should look like this:

bmpvieira

getCoordinates <- function(genus) {
  table1 <- read.csv('http://bmpvieira.github.io/temp/alabamaants-myrmicinaepheidole_obscurithorax.csv', h=T)
  table2 <- read.csv('http://bmpvieira.github.io/temp/allantwebants-myrmicinaesolenopsis_invicta.csv', h=T)
  mergedtable <- # put code here to merge table1 and table2
  # Once you have the merged table:
  # 1. Subset the table to a new one with only the rows that match the Genus provided by the argument of the function
  # 2. Limit the new one to only the columns DateCollectedStart, LocLatitude and LocLongitude.
  # 3. Remove rows that have NA values
  # 4. return the resulting table
}

bmpvieira

bionode-ncbi search genome Solenopsis invicta | tool-stream extractProperty assemblyid | bionode-ncbi search assembly - | tool-stream extractProperty uid | bionode-ncbi link assembly bioproject - | tool-stream extractProperty destUID | bionode-ncbi link bioproject sra - | tool-stream extractProperty destUID | bionode-ncbi search sra - | grep -e 20kb -e 8kb| tool-stream extractProperty uid24418

# Gives:
#23917
#23918
#23919
#23920
#23951
#23952
#23953

bmpvieira

var fasta = require('bionode-fasta')
var data = ">contig1\nAGTCGATCTACGTA\nATGATCATGCGTAC\n>contig2\nAGTACGTACTGCATG\ACTGCATCG\n"
var parser = fasta.obj() // Returns objects
      
parser.write(data)
parser.end()
      
parser.on('data', function(data) { console.log(data) })