Daniel E Cook danielecook

OS X Screencast to animated GIF

This gist shows how to create a GIF screencast using only free OS X tools: QuickTime, ffmpeg, and gifsicle.

Instructions

To capture the video (filesize: 19MB), using the free "QuickTime Player" application:

Project Title

One Paragraph+ describing the project goes here. For example: This is a README template you would use to describe a scientific or data analysis project. Provide an overview of the goals of the project, how data was obtained, and other important details others or you in 6 months should be aware of.

Data

Describe the dataset in more detail here if necessary

Data Contact

	function check_file {
	if [ ! -s "$1" ]
	then
	echo "$1 not found"
	fi
	}
	export -f check_file

	# List bams with a missing bai index
	ls -1 *.bam \| parallel check_file {}.bai

	$(patsubst %.vcf,%.vcf.gz,$(wildcard /.vcf)) \
	$(patsubst %.vcf.gz,%.vcf.gz.csi,$(wildcard /.vcf.gz))
	# Gzip VCFs and index if not present
	%.vcf.gz: %.vcf
	# gzipping $<
	bcftools view --output-type z $< > $@

	%.vcf.gz.csi: %.vcf.gz
	bcftools index $<

	slugify <- function(str) {
	# Function for cleaning up column names
	str %>%
	stringr::str_replace_all("[^a-zA-Z0-9-]", "_") %>%
	stringr::str_replace_all("-+", "_") %>%
	stringr::str_replace("[_]{2,50}", "_") %>%
	stringr::str_replace("_$", "") %>%
	tolower()
	}

	rows <- function(tab, idx=TRUE) {
	# Set idx to attach an index column
	if (is.na(tab) \|\| is.null(tab) \|\| nrow(tab) == 0) {
	return(list())
	}
	lapply(seq_len(nrow(tab)),
	function(i) {
	row <- unclass(tab[i,,drop=F])
	if (idx) {
	row$idx <- i

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

	# https://stackoverflow.com/questions/10103619/unix-merge-many-files-while-deleting-first-line-of-all-files#10103758
	tail -q -n +2 file1 file2 file3

	srun --ntasks=1 --cpus-per-task=3 --mem=4G --pty bash