Konrad Förstner konrad

I hereby claim:

I am konrad on github.
I am konradfoerstner (https://keybase.io/konradfoerstner) on keybase.
I have a public key whose fingerprint is 1D28 0E83 48EF 71FB 2975 8C68 C170 F2F8 3E02 D9A1

To claim this, I am signing this object:

I hereby claim:

I am konrad on github.
I am konradfoerstner (https://keybase.io/konradfoerstner) on keybase.
I have a public key whose fingerprint is 5801 2301 E981 C65D E0DB C0A1 41E6 AF4E DF9D B3D3

To claim this, I am signing this object:

	main(){
	upgrade_and_install_packages
	install_segemehl
	install_reademption
	}

	upgrade_and_install_packages(){
	sudo apt-get update
	sudo apt-get upgrade --assume-yes
	sudo apt-get install --assume-yes \

	#!/usr/bin/python

	# medline_search.py
	#
	# Small script to retrieve data of all publications of a given journal in
	# a given time frame from MEDLINE
	#
	# 2014 - Konrad Förstner <[email protected]>
	#
	# To the extent possible under law, the author have dedicated all

	import argparse
	from Bio import SeqIO

	parser = argparse.ArgumentParser(
	description="Split a multi entry fasta file into several files "
	"with one entry")
	parser.add_argument("input_file")
	parser.add_argument("output_prefix")
	args = parser.parse_args()

	from TwitterSearch import *
	import json

	try:
	tso = TwitterSearchOrder()
	tso.set_keywords(['#BOSC2015'])
	# Please replace with your credentials
	ts = TwitterSearch(
	consumer_key='REPLACE_ME',
	consumer_secret='REPLACE_ME',

	# Problem: You have a NCBI GEO accession and would like to get the URL of the SRA file that contains the sequencing data.
	# The sed command that removes the last characer of the string is essential as there is a invisible character that messes up the
	# downstream steps otherwise.

	GEO_ACCESSION="GSM1655353" # set you GEO accession here
	SRA_FTP_URL=$(curl "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=${GEO_ACCESSION}&targ=self&form=text&view=brief" 2>/dev/null \| grep ftp-trace.ncbi.nlm.nih.gov \| cut -c 32-\| sed 's/.$//')
	FTP_SUB_FOLDER=$(ncftpls ${SRA_FTP_URL}/)
	SRA_FILE=$(ncftpls ${SRA_FTP_URL}/${FTP_SUB_FOLDER}/)
	echo $GEO_ACCESSION ${SRA_FTP_URL}/${FTP_SUB_FOLDER}/${SRA_FILE}

	# Search for all mp3 and ogg files in my music folder and use mplayer to play in random order
	mplayer -shuffle -playlist $(find $MY_MUSIC_FOLDER -name "ogg" -o -name "mp3")

	FROM ubuntu:16.04

	RUN apt-get update && apt-get dist-upgrade -y
	RUN apt-get install -y curl wget git ruby python3 sra-toolkit snakemake libssl-dev libcurl4-openssl-dev libxml2-dev

	WORKDIR /root
	RUN wget https://github.com/pachterlab/kallisto/releases/download/v0.43.0/kallisto_linux-v0.43.0.tar.gz && \
	tar xzf kallisto_linux-v0.43.0.tar.gz && \
	mv kallisto_linux-v0.43.0/kallisto /usr/bin/ && \
	rm -rf kallisto_linux-v0.43.0 kallisto_linux-v0.43.0.tar.gz