Roman Hillje romanhaa

## run.sh
# https://macos-defaults.com/
# https://www.defaults-write.com

# reset with: defaults delete -g <FEATURE>

# dock
# position
defaults write com.apple.dock "orientation" -string "right"
# icon size
defaults write com.apple.dock "tilesize" -int "36"

## run.sh
grep --color=always -e "^" -e <SEARCH_TERM> <FILE>

## run.sh
# copy directory from A to B
rsync -ah --info=progress2 <DIR_SOURCE> <DIR_TARGET>

# copy directory from A into B
rsync -ah --info=progress2 <DIR_SOURCE> <PARENT_OF_DIR_TARGET>/

# copy content of directory A into B
rsync -ah --info=progress2 <DIR_SOURCE>/ <DIR_TARGET>/

# copy directory from A to B on remote machine

## run.sh
less -r <FILE>

## run.sh
iconv -f ISO-8859-1 -t UTF-8 -o <OUTPUT_FILE> <INPUT_FILE>

## run.sh
# convert Docker container to Singularity format
singularity build cell_ranger_3.1.0.sif docker://romanhaa/cell_ranger:3.1.0

# create index for Cell Ranger
# - modify "/hpcnfs" to your file system
singularity exec --bind /hpcnfs cell_ranger_3.1.0.simg \
cellranger mkref \
--genome=cell_ranger_3.1.0 \
--fasta=GRCh38.primary_assembly.genome.fa \
--genes=gencode.v32.annotation.gtf \

## alluvial.R
library("tidyverse")
library("ggalluvial")

# original data
# every genomic bin of 200bp is assigned one of 8 possible chromatin states
# note that group1-3 are factors
input_data
# A tibble: 855,156 x 4
#    bin            group1 group2 group3
#    <chr>          <fct>  <fct>  <fct>

## index.html
<!DOCTYPE html>
<html>
  <head>
    <meta http-equiv="X-UA-Compatible" content="chrome=1" />
    <meta http-equiv="Content-Type" content="text/html;charset=utf-8"/>
    <meta http-equiv="Access-Control-Allow-Origin" content="*"/>
    <meta charset="utf-8">
    <script src="https://d3js.org/d3.v3.min.js"></script>
  </head>
  <style>

## index.html
<!doctype HTML>
<meta charset = 'utf-8'>
<html>
  <head>

    <script src='//ramnathv.github.io/rCharts/libraries/widgets/polycharts/js/polychart2.standalone.js' type='text/javascript'></script>

    <style>
    .rChart {
      display: block;
	# https://macos-defaults.com/
	# https://www.defaults-write.com

	# reset with: defaults delete -g <FEATURE>

	# dock
	# position
	defaults write com.apple.dock "orientation" -string "right"
	# icon size
	defaults write com.apple.dock "tilesize" -int "36"
	# copy directory from A to B
	rsync -ah --info=progress2 <DIR_SOURCE> <DIR_TARGET>

	# copy directory from A into B
	rsync -ah --info=progress2 <DIR_SOURCE> <PARENT_OF_DIR_TARGET>/

	# copy content of directory A into B
	rsync -ah --info=progress2 <DIR_SOURCE>/ <DIR_TARGET>/

	# copy directory from A to B on remote machine
	# convert Docker container to Singularity format
	singularity build cell_ranger_3.1.0.sif docker://romanhaa/cell_ranger:3.1.0

	# create index for Cell Ranger
	# - modify "/hpcnfs" to your file system
	singularity exec --bind /hpcnfs cell_ranger_3.1.0.simg \
	cellranger mkref \
	--genome=cell_ranger_3.1.0 \
	--fasta=GRCh38.primary_assembly.genome.fa \
	--genes=gencode.v32.annotation.gtf \
	library("tidyverse")
	library("ggalluvial")

	# original data
	# every genomic bin of 200bp is assigned one of 8 possible chromatin states
	# note that group1-3 are factors
	input_data
	# A tibble: 855,156 x 4
	# bin group1 group2 group3
	# <chr> <fct> <fct> <fct>
	<!DOCTYPE html>
	<html>
	<head>
	<meta http-equiv="X-UA-Compatible" content="chrome=1" />
	<meta http-equiv="Content-Type" content="text/html;charset=utf-8"/>
	<meta http-equiv="Access-Control-Allow-Origin" content="*"/>
	<meta charset="utf-8">
	<script src="https://d3js.org/d3.v3.min.js"></script>
	</head>
	<style>
	<!doctype HTML>
	<meta charset = 'utf-8'>
	<html>
	<head>

	<script src='//ramnathv.github.io/rCharts/libraries/widgets/polycharts/js/polychart2.standalone.js' type='text/javascript'></script>

	<style>
	.rChart {
	display: block;