Sebastian Kurscheid skurscheid

Rerun rules with code changes.

  snakemake -R `snakemake --list-code-changes`

Rerun rules with any changes

  snakemake -R `snakemake --list-version-changes --list-code-changes --list-input-changes`

Most VPN Services are Terrible

Short version: I strongly do not recommend using any of these providers. You are, of course, free to use whatever you like. My TL;DR advice: Roll your own and use Algo or Streisand. For messaging & voice, use Signal. For increased anonymity, use Tor for desktop (though recognize that doing so may actually put you at greater risk), and Onion Browser for mobile.

This mini-rant came on the heels of an interesting twitter discussion: https://twitter.com/kennwhite/status/591074055018582016

tmux shortcuts & cheatsheet

start new:

tmux

start new with session name:

tmux new -s myname

	condaPackages <- function(x){
	lapply(names(x$otherPkgs), function(y){
	if ("git_url" %in% names(x$otherPkgs[[y]])){
	repo = "bioconductor-"
	} else {
	repo = "r-"
	}
	paste(repo, y, sep ="")
	})
	}

	// getTrueName.c
	// http://web.archive.org/web/20100110234300/http://www.macosxhints.com/dlfiles/getTrueName.txt
	//
	// DESCRIPTION
	// Resolve HFS and HFS+ aliased files (and soft links), and return the
	// name of the "Original" or actual file. Directories have a "/"
	// appended. The error number returned is 255 on error, 0 if the file
	// was an alias, or 1 if the argument given was not an alias
	//
	// BUILD INSTRUCTIONS

	#!/usr/bin/env python3
	'''
	gtf2bed.py converts GTF file to BED file.
	Usage: gtf2bed.py {OPTIONS} [.GTF file]

	History
	Nov.5th 2012:
	1. Allow conversion from general GTF files (instead of only Cufflinks supports).
	2. If multiple identical transcript_id exist, transcript_id will be appended a string like "_DUP#" to separate.
	'''

	ctrl-z
	bg

	touch /tmp/stdout
	touch /tmp/stderr
	gdb -p $!

	# In GDB
	p dup2(open("/tmp/stdout", 1), 1)
	p dup2(open("/tmp/stderr", 1), 2)

	# use ImageMagick convert
	# the order is important. the density argument applies to input.pdf and resize and rotate to output.pdf
	convert -density 90 input.pdf -rotate 0.5 -attenuate 0.2 +noise Multiplicative -colorspace Gray output.pdf