Ismail Moghul IsmailM

Bedtools Cheatsheet

General:

Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.

Access macOS localhost from IE or Edge within Parallels Desktop

This issue is so infuriating that I'm going to take some time to write about it.

MOST IMPORTANT. Your local development server must be bound to IP address 0.0.0.0. Some do this by default, but many don't. You need to make sure that you run your local server with correct IP bindings. You may need to provide additional flags to your serve commands e.g. polymer serve --hostname domain.local, hugo serve --bind 0.0.0.0. If you use a named domain like domain.local, it has to be defined in /etc/hosts and pointing at 0.0.0.0.
My Parallels setting is using Shared Network, nothing special there.
Open macOS Terminal and type ifconfig. Look for the value under vnic0 > inet. It is typically 10.211.55.2.

tmux cheatsheet

As configured in my dotfiles.

start new:

tmux

start new with session name:

Each of these commands will run an ad hoc http static server in your current (or specified) directory, available at http://localhost:8000. Use this power wisely.

Discussion on reddit.

Python 2.x

$ python -m SimpleHTTPServer 8000

tmux shortcuts & cheatsheet

start new:

tmux

start new with session name:

tmux new -s myname

	http://stackoverflow.com/questions/22667401/postgres-json-data-type-rails-query
	http://stackoverflow.com/questions/40702813/query-on-postgres-json-array-field-in-rails

	#payload: [{"kind"=>"person"}]
	Segment.where("payload @> ?", [{kind: "person"}].to_json)

	#data: {"interest"=>["music", "movies", "programming"]}
	Segment.where("data @> ?", {"interest": ["music", "movies", "programming"]}.to_json)
	Segment.where("data #>> '{interest, 1}' = 'movies' ")
	Segment.where("jsonb_array_length(data->'interest') > 1")

	#!/bin/sh

	if [ "$1" == "" ]; then
	echo "Usage: $0 <folder to compress>"
	exit
	fi

	NAME=`basename $1`

	tar -c --use-compress-program=pigz -f $NAME.tar.gz $NAME

	# This is the sshd server system-wide configuration file. See
	# sshd_config(5) for more information.

	# This sshd was compiled with PATH=/usr/bin:/bin:/usr/sbin:/sbin

	# The strategy used for options in the default sshd_config shipped with
	# OpenSSH is to specify options with their default value where
	# possible, but leave them commented. Uncommented options change a
	# default value.

	tell application "Safari"
	repeat with theSafariWindow in windows
	tell application "Google Chrome" to set theChromeWindow to make new window
	repeat with theSafariTab in theSafariWindow's tabs
	set theURL to URL of theSafariTab
	tell application "Google Chrome"
	set theChromeTab to make new tab at end of tabs of theChromeWindow
	set URL of theChromeTab to theURL
	end tell
	end repeat

	wget http://www.openbioinformatics.org/annovar/download/annovar.latest.tar.gz.mirror
	tar xzvf annovar.tar.gz
	cd annovar

	# download databases (goes to UCSC)
	./annotate_variation.pl -buildver hg19 -downdb 1000g2010nov humandb
	./annotate_variation.pl -buildver hg19 -downdb avsift humandb
	./annotate_variation.pl -buildver hg19 -downdb refGene humandb
	./annotate_variation.pl -buildver hg19 -downdb mce46way humandb/
	./annotate_variation.pl -buildver hg19 -downdb snp131 humandb/