M. Foos mfoos

Project Title

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Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

Opening and closing an SSH tunnel in a shell script the smart way

I recently had the following problem:

From an unattended shell script (called by Jenkins), run a command-line tool that accesses the MySQL database on another host.
That tool doesn't know that the database is on another host, plus the MySQL port on that host is firewalled and not accessible from other machines.

We didn't want to open the MySQL port to the network, but it's possible to SSH from the Jenkins machine to the MySQL machine. So, basically you would do something like

ssh -L 3306:localhost:3306 remotehost

	---
	title: "Printing chunk engine via hook"
	output: github_document
	---

	```{r setup, include=FALSE}
	library(knitr)
	opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)

	print_engine_hook <- function(before, options, envir) {

	# All this is implemented (plus bugfixes!) in the ggnewscale package:
	# https://github.com/eliocamp/ggnewscale
	# If you have any issues, I prefer it if you send them as issues here:
	# https://github.com/eliocamp/ggnewscale/issues

	#' Allows to add another scale
	#'
	#' @param new_aes character with the aesthetic for which new scales will be
	#' created
	#'

	library(shiny)

	# WARNING: This sketch does not make proper use of the "state" parameter.
	# Doing so usually involves using cookies, which can be done with the
	# Rook package but I have not done that here. If you choose to use this
	# approach in production, please check the state parameter properly!

	APP_URL <- if (interactive()) {
	# This might be useful for local development. If not, just hardcode APP_URL
	# to the deployed URL that you'll provide a few lines below.

	---
	output:
	html_document
	---

	```{r setup, echo = FALSE}
	knitr::opts_chunk$set(
	collapse = TRUE,
	comment = "#>"
	)

	import luigi
	from luigis_monkey_wrench import *

	REF='human_17_v37.fasta'
	INDIVIDUALS=['NA06984','NA07000']
	SAMPLES=['1','2']
	BASENAME='.ILLUMINA.low_coverage.17q_'
	PICARDDIR='/sw/apps/bioinfo/picard/1.69/kalkyl/'
	KNOWNSITES='/proj/g2014207/labs/gatk/ALL.chr17.phase1_integrated_calls.20101123.snps_indels_svs.genotypes.vcf'

	## RNA-seq analysis with DESeq2
	## Stephen Turner, @genetics_blog

	# RNA-seq data from GSE52202
	# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
	# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

	# Import & pre-process ----------------------------------------------------

	# Import data from featureCounts