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Niklas Reimer nr23730

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nr23730 / installSingularityDebianUbuntu
Created October 27, 2020 14:58
Install Singularity on Debian based systems like Debian, Ubuntu, Mint, etc. that use apt as package manager.
#!/bin/bash
export GOVERSION=1.15.3
export SINGULARITYVERSION=3.6.4
sudo apt-get update && sudo apt-get install -y \
build-essential \
uuid-dev \
libgpgme-dev \
squashfs-tools \
libseccomp-dev \
@nr23730
nr23730 / setup.sh
Last active April 28, 2020 19:13
Overleaf Docker + TeX Live Full + Pygments + Nonfreefonts
#!/bin/bash
docker exec sharelatex tlmgr option repository ftp://tug.org/historic/systems/texlive/2019/tlnet-final
docker exec sharelatex tlmgr update --self --verify-repo=none
docker exec sharelatex tlmgr install scheme-full --verify-repo=none
docker exec sharelatex wget http://tug.org/fonts/getnonfreefonts/install-getnonfreefonts
docker exec sharelatex texlua install-getnonfreefonts
docker exec sharelatex getnonfreefonts --sys -a
docker exec sharelatex apt-get install python-pygments -y
docker exec sharelatex tlmgr update --all --verify-repo=none
@nr23730
nr23730 / chr_synonyms.txt
Created October 15, 2019 18:28
If you try to use the ucsc hg19 fasta with Ensemble VEP (GRCh37) you'll get errors/warnings. They are caused because the haplotypes have different identifiers. To solve this you can append the content of this gist to the end of your chr_synonyms.txt file in the vep data directory. I mapped them by comparing the index files (.fai).
MT chrM
GL000191.1 chr1_gl000191_random
GL000192.1 chr1_gl000192_random
GL000193.1 chr4_gl000193_random
GL000194.1 chr4_gl000194_random
GL000195.1 chr7_gl000195_random
GL000196.1 chr8_gl000196_random
GL000197.1 chr8_gl000197_random
GL000198.1 chr9_gl000198_random
GL000199.1 chr9_gl000199_random
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nr23730 / MLO-GPT-M1S.ino
Created October 12, 2019 18:16
MLO-GPT-M1S.ino mit Reconnect nach Verbindungsverlust
#include <ModuleSerialCore.h>
#include <ModuleSerialGprs.h>
#include <ModuleSerialGps.h>
#define SIM_APN "web.vodafone.de"
#define SIM_APN_USERNAME ""
#define SIM_APN_PASSWORD ""
String MLO_USERNAME = "Organisation";
String MLO_TID = "tid";