One Paragraph of project description goes here
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.
--- | |
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 |
I recently had the following problem:
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