Joe Thorley joethorley

A computational biologist who performs Bayesian analyses using R, STAN and JAGS.

joethorley / project-create.sh

Created October 24, 2018 20:46 — forked from francoisromain/project-create.sh

A bash script to create a Git post-receive hook to deploy after a Git push

	#!/bin/bash

	# Call this file with `bash ./project-create.sh project-name [service-name]`
	# - project-name is mandatory
	# - service-name is optional

	# This will creates 4 directories and a git `post-receive` hook.
	# The 4 directories are:
	# - $GIT: a git repo
	# - $TMP: a temporary directory for deployment

joethorley / update_git_repos.sh

Created May 2, 2017 22:33 — forked from douglas/update_git_repos.sh

Update all git repositories under a base directory

	#!/bin/bash

	# store the current dir
	CUR_DIR=$(pwd)

	# Let the person running the script know what's going on.
	echo "\n\033[1mPulling in latest changes for all repositories...\033[0m\n"

	# Find all git repositories and update it to the master latest revision
	for i in $(find . -name ".git" \| cut -c 3-); do

joethorley / dprint.R

Last active January 10, 2017 18:49

print when debugging

	dprint <- function(x, note = NULL, do = getOption("dprint.do", TRUE)) {
	if (!do) return(invisible())
	if (!is.null(note))
	cat("\n", note, "\n")
	cat("\n", deparse(substitute(x)), ": \n", sep = "")
	print(x)
	}

joethorley / normalize.R

Created January 4, 2017 23:29

normalize

joethorley / osx_install.sh

Created April 4, 2016 19:00 — forked from t-io/osx_install.sh

Install most of my Apps with homebrew & cask

	#!/bin/sh
	echo Install all AppStore Apps at first!
	# no solution to automate AppStore installs
	read -p "Press any key to continue... " -n1 -s
	echo '\n'

	echo Install and Set San Francisco as System Font
	ruby -e "$(curl -fsSL https://raw.github.com/wellsriley/YosemiteSanFranciscoFont/master/install)"
	echo Install Homebrew, Postgres, wget and cask
	ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

joethorley / brewR

Last active April 18, 2016 19:44

brewing R

	First of all made sure that command line developer tools (but not XCode were installed)
	<http://railsapps.github.io/xcode-command-line-tools.html>

	```
	brew tap caskroom/cask

	brew install Caskroom/cask/xquartz
	brew cask install java

	brew cask install basictex

joethorley / brewbasictex

Created April 1, 2016 23:46

Install basictex using brew for R

	brew tap caskroom/cask

	brew cask install basictex
	sudo tlmgr update --self
	sudo tlmgr update --all
	sudo tlmgr install titling framed inconsolata

joethorley / ext.R

Last active August 29, 2015 13:56

Wrappers to get, remove, replace, add and test file name extensions

	library(tools)
	library(assertthat)

	#' @title Filename extension utilities
	#'
	#' @description Replaces, adds or removes (rm) extensions from filenames or test whether
	#' filename has an extension or is a filename with a particular extension.
	#' Functions are primarily wrappers
	#' on the tools package functions \code{file_ext} and \code{file_path_sans_ext}.
	#'