konrad

#!/usr/bin/env bash

#
# Script to run within the NixOS install image.
# 


set -o errexit

readonly SWAP_SIZE_IN_GB=1

konrad

#!/bin/env bash
#
# Copyright 2020 Konrad Förstner
#
# Permission to use, copy, modify, and/or distribute this software for
# any purpose with or without fee is hereby granted, provided that the
# above copyright notice and this permission notice appear in all
# copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL

konrad

#!/bin/bash                                                                                                                                                                                                                                                                                                                                                                                 

# Small script to combine some photos, cut a mp3 file into two pieces,                                                                                                                                                                                                                                                                                                                      
# fade in and out and merge everything. Rather specific so needs to be                                                                                                                                                                                               

konrad

#!/usr/bin/env bash

# Returns a BibTeX (www.bibtex.org) entry for one or more given DOIs
# (https://www.doi.org/).
#
# Call it like this:
#
# $ doi2bibtex.sh 10.1093/bioinformatics/btu533
#
# Can also be used for several DOIs at once:

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:

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

27203499
27203498
27187993
27147017
27115821
27111981
27111968
27082204
27078543
27048000

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

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

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',