konrad

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 \

konrad

#!/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 <konrad.foerster@uni-wuerzburg.de>
#
#  To the extent possible under law, the author have dedicated all

konrad

# 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")

konrad

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()

konrad

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',

konrad

Keybase proof

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:

konrad

# 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}

konrad

27203499
27203498
27187993
27147017
27115821
27111981
27111968
27082204
27078543
27048000

konrad

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

konrad

Keybase proof

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: