Anton Kratz antonkratz

Delete all lines in the file myfile that contain the string foobar:

sed -i '/foobar/d' myfile

Cytoscape 3.7.1

the layout is too dense and I want to expand the layout

Layout --> Node layout Tools --> Scale:

when I zoom out, the text on the label dissappears

You might run into a situation where git log, man man display absolutely nothing. This could be b/c bash forgot the PAGER variable. How this is possible is beyond me. You must reset the PAGER variable and then it will work again:

export PAGER=less

Disable the caps lock key entirely

Ubuntu

setxkbmap -option "caps:none"

Building a separate database enables you to locate files on sshfs-mounted filesystems

The find command is very slow. locate is much faster, but relies on a database, which is typically build nightly. Often I have mounted remote filesystems using sshfs. By default, the database is not build for sshfs-mounted filesystems.

Build an mlocate database for the sshfs-mounted dir /home/kratz/mpoints/cellar (see below for cron version):

updatedb -l 0 -o ~/.cellar.db -U /home/kratz/mpoints/cellar

Installing R on your own machine

The main guide on how to install R for any flavour of linux, binary or from source, is at http://cran.stat.ucla.edu/

Three different pathways to a working install, from simple to hard:

use the distributions package manager (easiest but not the most recent version)
install binary (recommended)
compile and install from source

I am assuming you are on Ubuntu 16.04 LTS.

find . -type f -exec \
bash -c 'md5sum "$0" | grep -q b2a490745fe5fe8a41c0d1040faff507 && echo $0' {} \;

https://superuser.com/questions/653185/finding-a-file-by-md5sum

install graphviz: sfdp, gvmaps, mingle

# building gv from source
# otherwise: "Error: remove_overlap: Graphviz not built with triangulation library"

wget https://graphviz.gitlab.io/pub/graphviz/stable/SOURCES/graphviz.tar.gz
gunzip graphviz.tar.gz
tar xvf graphviz.tar

	# author: Anton Kratz
	# created: Mon Dec 17 19:08:48 PST 2018

	# Based on original code by Mike Yu which is at [1]. However [1] has various NDEX and other
	# code intermingled which is not necessary in this context. Also, I am building a similarity
	# table for DNA repair on the fly.

	# [1] https://github.com/michaelkyu/ddot/blob/master/examples/Process_the_Gene_Ontology.ipynb

	import requests