OnesimusUnbound

[T]he difference between a bad programmer and a 
good one is whether he considers his code or his 
data structures more important. Bad programmers 
worry about the code. Good programmers worry about 
data structures and their relationships. 
-- Linus Torvalds
~~~
Clarity and brevity sometimes are at odds. 
When they are, I choose clarity. 
-- Jacob Kaplan-Moss

kumabotz

# Stashing is a great way to pause what you’re currently working on and come 
# back to it later. For example, if you working on that awesome, brand new 
# feature but someone just found a bug that you need to fix. Add your changes to 
# the index using

  $ git add .

# Or add individual files to the index, your pick. Stash your changes away with:

  $ git stash

martijnvermaat

Download SRA run files for given sample names

Have all sample names in samples, one per line and run:

for sample in $(cat samples); do
    IFS=$'\n'
    for line in $(./sra-runs.py $sample); do
        echo $sample $line >> runs

done

SachaEpskamp

library("shiny")
library("foreign")

sloria

The Best of the Best Practices (BOBP) Guide for Python

A "Best of the Best Practices" (BOBP) guide to developing in Python.

In General

Values

• "Build tools for others that you want to be built for you." - Kenneth Reitz
• "Simplicity is alway better than functionality." - Pieter Hintjens

rmflight

#!/path/2/Rscript

# License: CC0 (just be nice and point others to where you got this)
# Author: Robert M Flight <rflight79@gmail.com>, github.com/rmflight
#
# This is a post-commit hook that after a successful commit subsequently increments the package version in DESCRIPTION
# and commits that. Analogous to the pre-commit at https://gist.github.com/rmflight/8863882, but useful if you only have
# good reasons for not doing it on the pre-commit.
#
# To install it, simply copy this into the ".git/hooks/post-commit" file of your git repo, change /path/2/Rscript, and make

LeCoupa

#!/bin/bash
#####################################################
# Name: Bash CheatSheet for Mac OSX
# 
# A little overlook of the Bash basics
#
# Usage:
#
# Author: J. Le Coupanec
# Date: 2014/11/04

jennybc

There are packages for this now!

2017-08-03: Since I wrote this in 2014, the universe, specifically Kirill Müller (https://github.com/krlmlr), has provided better solutions to this problem. I now recommend that you use one of these two packages:

• rprojroot: This is the main package with functions to help you express paths in a way that will "just work" when developing interactively in an RStudio Project and when you render your file.
• here: A lightweight wrapper around rprojroot that anticipates the most likely scenario: you want to write paths relative to the top-level directory, defined as an RStudio project or Git repo. TRY THIS FIRST.

I love these packages so much I wrote an ode to here.

I use these packages now instead of what I describe below. I'll leave this gist up for historical interest. 😆

jtpaasch

# -*- coding: utf-8 -*-

"""A simple tool to document how to control AWS resources.

AWS AUTHENTICATION
-------------------

In order to run any of the code below, you need a profile with AWS credentials
set up on your computer. It's very easy to do this. Google how to configure
your profile with boto3, or visit the docs:

quiver

Sometimes you want to retrieve EC2 insntances' region information.

You can query that information through instance metadata(169.254.169.254).

$ curl --silent http://169.254.169.254/latest/dynamic/instance-identity/document
{
  "privateIp" : "172.31.2.15",
  "instanceId" : "i-12341ee8",
  "billingProducts" : null,
 "instanceType" : "t2.small",