Automation for the People

Long ago, the first time I read "The Pragmatic Programmer", I read some advice that really stuck with me.

"Don't Use Manual Procedures".

This in the chapter on Ubiquitous Automation. To summarize, they want you to automate all the things.

The trouble was that I hadn't much of an idea how to actually go

Yixf-Self / clock.R

Created July 9, 2016 00:41 — forked from drewconway/clock.R

Generate an animated clock in R with ggplot2

	# Generate digitial clock face
	first.nine <- c('00', '01', '02', '03', '04', '05', '06', '07', '08', '09')
	hours <- c(first.nine, as.character(seq(10,23,1)))
	mins <- c(first.nine, as.character(seq(10,59,1)))
	time.chars.l <- lapply(hours, function(h) paste(h, ':', mins, sep=''))
	time.chars <- do.call(c, time.chars.l)

	# Generate analog clock face
	hour.pos <- seq(0, 12, 12/(12*60))[1:720]
	min.pos <-seq(0,12, 12/60)[1:60]

Yixf-Self / fastq_pair_filter.py

Created September 23, 2016 01:50 — forked from brentp/fastq_pair_filter.py

	#!/usr/bin/python
	"""
	%prog [options] pair_1.fastq pair_2.fastq

	filter reads from paired fastq so that no unmatching reads remain.
	output files are pair_1.fastq.trim and pair_2.fastq.trim
	see: http://hackmap.blogspot.com/2010/09/filtering-paired-end-reads-high.html
	"""
	from subprocess import Popen, PIPE
	import sys

Yixf-Self / bash-cheatsheet.sh

Created July 20, 2017 00:35 — forked from LeCoupa/bash-cheatsheet.sh

Bash CheatSheet for UNIX Systems

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

Yixf-Self / bash-cheat-sheet

Created July 20, 2017 00:43

BASH Cheat Sheet

	B A S H C H E A T S H E E T

	to page output forward (only): command filename \| more
	to page output forward & back: command filename \| less
	to print a dataset: lp datasetname (-d printerid) (-o landscape)

	USE OF QUOTATION MARKS
	echo "$varname" = echo The value of \$varname is \"$varname\"
	= echo "The value of \$varname is \"$varname\"."
	$fred='Four spaces between these words.'

Yixf-Self / fastqc.wdl

Created August 16, 2017 03:51 — forked from seandavi/fastqc.wdl

	task fastqc {
	File fastq

	command {
	fastqc ${fastq}
	}
	output {
	Array[File] results = glob("*html")
	}
	runtime

Yixf-Self / 000_geom_bag.r

Created September 3, 2017 00:47 — forked from benmarwick/000_geom_bag.r

Basic bagplot geom for ggplot2

	#' Bagplot
	#'
	#' The bag geom is useful for graphical summaries of scatterplots. It
	#' is effective at showing the location, spread, skewness, and
	#' outliers of a data set.
	#'
	#' A bagplot is a bivariate generalization of the well known boxplot. It
	#' was proposed by Rousseeuw, Ruts, and Tukey. This geom plots bagplots that
	#' are very similar to the one described in Rousseeuw et al. and
	#' uses code from their bagplot functions in the aplpack pacakge.

Yixf-Self / server.R

Created December 5, 2017 09:48 — forked from duxan/server.R

A Shiny/R app to display the Illumina human body map dataset. I have not included the expression data due to it's size (19Gb) but this should work with any RNA-seq data set analysed with a TopHat->Cufflinks->CuffDiff pipeline.

	library(shiny)
	library(deSolve)
	library(cummeRbund)

	# load cuffDiff data, must be in top dir and called cuffData.db:
	cuff = readCufflinks()

	shinyServer(function(input,output) {

	getData = reactive(function() {

Yixf-Self / memusg

Created January 18, 2018 09:46 — forked from netj/memusg

memusg -- Measure memory usage of processes

	#!/usr/bin/env bash
	# memusg -- Measure memory usage of processes
	# Usage: memusg COMMAND [ARGS]...
	#
	# Author: Jaeho Shin <[email protected]>
	# Created: 2010-08-16
	############################################################################
	# Copyright 2010 Jaeho Shin. #
	# #
	# Licensed under the Apache License, Version 2.0 (the "License"); #

Yixf-Self / findhao_rss_sources.xml

Created September 26, 2018 01:28 — forked from FindHao/findhao_rss_sources.xml

我的rss订阅源

	This XML file does not appear to have any style information associated with it. The document tree is shown below.
	<opml version="1.0">
	<head>
	<title>
	Subscriptions of find from Inoreader [https://www.inoreader.com]
	</title>
	</head>
	<body>
	<outline text="Blogs" title="Blogs">
	<outline text="cgnail's weblog" title="cgnail's weblog" type="rss" xmlUrl="http://cgnail.github.io/atom.xml" htmlUrl="http://cgnail.github.io/"/>

Yi Xianfu Yixf-Self

Automation for the People