zachcp

Useful Genomics Oneliners

The following commands sometimes require non-standard software like bioawk and seqtk.

rename scaffold headers with sequential numbers and lengths ("scaffold-N ")

bioawk -c fastx '{ print ">scaffold-" ++i" "length($seq)"\n"$seq }' < genome.fasta > new_genome.fasta

make association table of old and renamed scaffold names after above renaming command

Set the default size for new Docker for Mac disk images

UPDATE: The instructions here are no longer necessary! Resizing the disk image is now possible right from the UI since Docker for Mac Version 17.12.0-ce-mac49 (21995).

If you are getting the error: No space left on device

Configuring the qcow2 size cap is possible in the current versions:

# my disk is currently 64GiB

How to run Express inside an Electron app

You can run your Express app very easily inside your Electron app.

All you need to do is to:

place all the files of your Express app inside a new app folder in your_electron_app\resources\app
reconfigure the app.js file
refactor some relative pathes in your Express app

	Wheeler graphs

	Gagie, Manzini, Siren
	Theoretical Computer Science, 2017
	https://www.sciencedirect.com/science/article/pii/S0304397517305285

	Notes of a whiteboard presentation to the Bonsai team in Lille.
	These notes largely follow the paper.
	Rayan Chikhi, 2019

	#!/usr/bin/env python3

	import zipfile
	import sys
	import re
	import xml.etree.ElementTree as ET

	namespaces = {
	'a': 'http://schemas.openxmlformats.org/drawingml/2006/main',
	'r': 'http://schemas.openxmlformats.org/officeDocument/2006/relationships',

	'use strict';
	exports.handler = (event, context, callback) => {

	// Get request and request headers
	const request = event.Records[0].cf.request;
	const headers = request.headers;

	// Configure authentication
	const authUser = 'user';
	const authPass = 'pass';

	import requests
	import json

	####
	# inputs
	####
	username = ''

	# from https://github.com/user/settings/tokens
	token = ''

	(ns speakup.core
	(:require [rum.core :as rum]
	[cljs-react-material-ui.core :refer [get-mui-theme color]]
	[cljs-react-material-ui.icons :as ic]
	[cljs-react-material-ui.rum :as ui]
	[cljs-react-material-ui.chip-input.rum :refer [chip-input]]))

	(enable-console-print!)

	;; (println "This text is printed from src/speakup/core.cljs. Go ahead and edit it and see reloading in action.")

	FROM centos

	# following http://www.pacb.com/wp-content/uploads/2015/09/SMRT-Analysis-Software-Installation-v2.3.0.pdf

	MAINTAINER [email protected]

	ENV SMRT_ROOT=/opt/smrtanalysis/
	ENV SMRT_USER=smrtanalysis
	ENV SMRT_GROUP=smrtanalysis