Stian Lågstad stianlagstad

stianlagstad / getSequenceById.sh

Created February 3, 2016 12:23

Extract specific sequences from a fastq file with this bash oneliner

egrep -A 3 '@readid1|readid2|readid3' reads.fastq | sed '/^--$/d'

stianlagstad / pyodbc in Docker with MySQL and Oracle

Created December 21, 2017 21:47

This Dockerfile should get you going with pyodbc in Docker with the drivers to talk to MySQL and Oracle databases

	FROM python:3

	WORKDIR /usr/src/app

	# Copy over the drivers
	# MySQL ODBC Ansi
	COPY drivers/mysql-connector-odbc-5.3.9-linux-ubuntu16.04-x86-64bit.tar.gz .
	# Oracle 11.2
	COPY drivers/oracle-instantclient11.2-basic-11.2.0.4.0-1.x86_64.rpm .
	COPY drivers/oracle-instantclient11.2-odbc-11.2.0.4.0-1.x86_64.rpm .

stianlagstad / sortTestsByTimeTaken.sh

Created January 19, 2018 07:54

Using maven and surefire? This script will help you figure out which tests are slow.

	#!/bin/bash

	# This script goes through tests results in `target/surefire-reports` and sorts the results by the
	# amount of time they took. This is helpful to identify slow tests.

	set -e

	# Make sure the surefire folder exists
	if [ ! -d "target/surefire-reports" ]; then
	echo "The folder 'target/surefire-reports' doesn't exists. Please run tests before using this script."