Always be gitin'

Johan Viklund viklund

Always be gitin'

viklund / 00_init_k3d.sh

Last active December 10, 2019 10:16

Simple LocalEGA Helm setup

	#!/usr/bin/env bash
	source _script_source.sh
	set -e

	has_traefik_pods() {
	L=$(kubectl get pods -n kube-system -lapp=svclb-traefik 2>/dev/null \| wc -l)
	if [ $L -eq 0 ]; then
	false
	else
	true

viklund / Dockerfile

Last active December 3, 2019 13:37

Crypt4gh docker experiments

	FROM debian:10-slim

	## Otherwise Java won't install
	RUN mkdir -p /usr/share/man/man1

	RUN apt-get update \
	&& apt-get install -y gnupg2

	## This is to get openjdk-11-jre to install on -slim
	RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys EA8CACC073C3DB2A

viklund / calc_line_proportions.pl

Last active August 17, 2018 13:01

viklund / mathsheet.html

Last active March 23, 2018 21:37

viklund / remove_temp_files.nf

Created March 22, 2018 10:16

	// Hack nextflow workflow that removes intermediate files generated
	// by process A once process B is done with the files

	inputA = Channel.from(
	[1, file('f1')],
	[2, file('f2')],
	[3, file('f3')],
	[4, file('f4')],
	[5, file('f5')])

viklund / clean-localega-repo.sh

Last active January 15, 2018 10:29

	#!/usr/bin/env bash

	## Backup clone
	git clone [email protected]:NBISweden/LocalEGA.git LocalEGA-backup-$(date +"%Y-%m-%d_%H:%M:%S")

	## Clone it
	[ -d LocalEGA-cleaning ] && rm -rf LocalEGA-cleaning
	git clone [email protected]:NBISweden/LocalEGA.git LocalEGA-cleaning
	cd LocalEGA-cleaning

viklund / setup_docker_database.sh

Created November 27, 2017 15:09

	#!/bin/bash

	MYSQL_PORT=3366
	MYSQL_HOST=127.0.0.1
	MYSQL_PASS=rootpw

	# Start a mysql instance with docker for example like this:
	docker volume create swefreq-mysql-data
	docker run -v swefreq-mysql-data:/var/lib/mysql --rm --name mysql -e MYSQL_ROOT_PASSWORD=$MYSQL_PASS -d -p $MYSQL_PORT:3306 mysql

viklund / markov.py

Created October 18, 2017 09:09

	import markovify
	import json
	import os

	users = json.load(open('slack/users.json'))

	user = ''
	for u in users:
	if u['name'] == 'viklund':
	user = u['id']

viklund / number_of_commits.rb

Created October 16, 2017 13:49

Number of commits per repo on the NBISweden github repo

viklund / Filter blast result with awk

Created June 7, 2016 09:45

	$ awk '$4>50 && $3>90 && F[$1]++ < 1{print}' blast_result

	$4 is column 4 i.e. length, larger than 50bp

	$3 percent identity bigger than 90

	F[$1]++ < 1 is the tricky part. We count upwards for each query we find and as long as the number
	is less than 1 it is true, since the ++ is after the F[$1] the value will be zero the first time
	and 1 the second time and so on.