Rik Smith-Unna blahah

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blahah / quickscrape_provision.sh

Last active August 29, 2015 14:05

quickscrape Vagrant provisioning

	# install basic tools
	sudo apt-get install -y curl build-essential

	# install NVM
	curl https://raw.githubusercontent.com/creationix/nvm/v0.13.1/install.sh \| bash
	. /home/vagrant/.profile

	# install Node.js
	nvm install v0.10.30
	nvm use 0.10

blahah / dev_setup.sh

Last active August 29, 2015 14:05

OSX dev setup (wip)

	# Ask for the administrator password upfront
	sudo -v

	# homebrew
	ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
	brew doctor

	# Ruby Version Manager & latest Ruby
	\curl -sSL https://get.rvm.io \| bash -s stable --ruby
	source ~/.rvm/scripts/rvm

blahah / markov.jl

Created August 4, 2014 11:43

Markov chain generator in Julia

	# Type representing a Markov chain generator.
	# It stores an array of the possible states in the chain,
	# and a transition matrix defining the probabilities
	# of moving from one state to another.
	type MarkovGenerator
	states::Array{Int}
	transmat::Array{Float64}
	end

	# Given the current state, get the next state of a Markov chain

blahah / trim-batch.rb

Created July 29, 2014 22:30

Trimmomatic wrapper script

	#!/usr/bin/env ruby

	#
	# trim-batch
	#
	# Take in a set of fastq files and run trimmomatic on each
	#
	# You MUST specify the location of the trimmomatic JAR
	#
	# Richard Smith-Unna (rds45@cam.ac.uk)

blahah / express.rb

Created July 29, 2014 07:45

eXpress script

	#!/usr/bin/env ruby

	require 'csv'
	require 'rubygems'
	require 'trollop'

	class Express
	attr_accessor :bundle_id,:target_id,:length,:eff_length,:tot_counts,:uniq_counts
	attr_accessor :est_counts,:eff_counts,:ambig_distr_alpha,:ambig_distr_beta,:fpkm
	attr_accessor :fpkm_conf_low,:fpkm_conf_high,:solvable,:tpm

blahah / zoosys_evo_pdfs.txt

Created July 23, 2014 14:11

Zoosystematics and Evolution all PDFs evar!

	http://onlinelibrary.wiley.com/doi/10.1002/zoos.201300006/pdf
	http://onlinelibrary.wiley.com/doi/10.1002/zoos.201300007/pdf
	http://onlinelibrary.wiley.com/doi/10.1002/zoos.201300008/pdf
	http://onlinelibrary.wiley.com/doi/10.1002/zoos.201300009/pdf
	http://onlinelibrary.wiley.com/doi/10.1002/zoos.201300010/pdf
	http://onlinelibrary.wiley.com/doi/10.1002/zoos.201300011/pdf
	http://onlinelibrary.wiley.com/doi/10.1002/zoos.201300012/pdf
	http://onlinelibrary.wiley.com/doi/10.1002/zoos.201300013/pdf
	http://onlinelibrary.wiley.com/doi/10.1002/zoos.201300014/pdf
	http://onlinelibrary.wiley.com/doi/10.1002/zoos.201300015/pdf

blahah / setup_js_tests.sh

Last active August 29, 2015 14:03

Set up journal_scrapers test generation environment on a DigitalOcean VM

	apt-get install -y software-properties-common build-essential python-software-properties libfontconfig1 git
	add-apt-repository -y ppa:chris-lea/node.js
	apt-get update
	apt-get install -y nodejs
	npm install --global quickscrape
	\curl -sSL https://get.rvm.io \| bash -s stable --ruby
	gem install trollop
	git clone https://github.com/ContentMine/journal-scrapers.git

blahah / gist:5d7502d101b7b1282c41

Last active August 29, 2015 14:02

shorten multiple URLs with the bit.ly API in a unix one-liner

	# have your URLs in a file called URLS
	parallel -j1 curl -v 'http://api.bit.ly/shorten?version=2.0.1\&longUrl={}\&login=bitlyapidemo\&apiKey=ABC123' < URLS

blahah / install_phantomJS.sh

Last active November 17, 2016 18:55

linux install phantomJS

	echo "installing phantomJS"
	if [ `getconf LONG_BIT` = "64" ]
	then
	echo "64-bit system detected"
	PHANTOMVER=phantomjs-1.9.7-linux-x86_64
	else
	echo "32-bit system detected"
	PHANTOMVER=phantomjs-1.9.7-linux-i686
	fi
	wget https://bitbucket.org/ariya/phantomjs/downloads/$PHANTOMVER.tar.bz2 && \

blahah / install_qs.sh

Last active August 29, 2015 14:02

quickscrape install debian/ubuntu

	if [[ $(uname -v) =~ Debian ]]; then
	echo "Debian detected: installing backports"
	echo "deb http://ftp.us.debian.org/debian wheezy-backports main" >> /etc/apt/sources.list
	apt-get update
	apt-get install -y nodejs
	apt-get install -y nodejs-legacy
	curl --insecure https://www.npmjs.org/install.sh \| bash
	fi
	if [[ $(uname -v) =~ Ubuntu ]]; then
	echo "Ubuntu detected: using Chris Lea's PPA repo"