nylander

#!/bin/bash

# Convert Markdown to PDF (beamer) using pandoc
# Last modified: mån sep 07, 2020  03:05
# Johan Nylander

for f in "$@"
do
  echo -n "Converting $f ..."
  g=${f%.md}.pdf

nylander

#!/bin/bash

# Convert Markdown to PDF using pandoc
# Last modified: tor aug 20, 2020  02:51
# Johan Nylander
# TODO: set mainfont to allow for special characters () -V 'mainfont:xxx xx'

hash pandoc 2>/dev/null || { echo >&2 "Cannot find pandoc. Aborting."; exit 1; }

for f in "$@"

nylander

FILE: fas2nex.stdinout

        USAGE: ./fas2nex.stdinout <input>

nylander

Loops

• Last modified: Mon Oct 13, 2025
• Sign: Johan Nylander

Description

Examples of doing the same thing on many input files. Often called "loops" (since after being done with the first file, we return to the binning of our commands and do it all over again).

nylander

#!/usr/bin/env Rscript
# File: summary
# Description: Summarize data from stdin as min, max, mean, median
# Requirements: R
# Usage example: for i in $(seq 1 100); do echo $RANDOM; done | summary
# 288 32697 14644.19 14256
a <- scan(file("stdin"), c(0), quiet=TRUE);
cat(min(a), max(a), mean(a), median(a), "\n");

nylander

#! /bin/bash
# blast2fasta
# Parse output from blast where we have sseq as the last column.
# For example (argument to blastn): "-outfmt '6 qseqid sseq'".
# Reads from file, writes to stdout.
# By Johan Nylander
# 2023-Oct-10
# Usage: blast2fasta.sh file
file=$1
awk '{printf ">%s", $1; for(i=2;i<NF;i++) printf " %s", $i; printf "\n%s\n", $NF}' "$file"

nylander

#!/usr/bin/env perl

=pod

=encoding utf8

=head1 NAME

create_sample_sheet.pl - Create sample sheet from NGI delivery

nylander

#!/usr/bin/env bash

# Start/stop FortiClient VPN
# Last modified: ons mar 15, 2023  03:47
# Sign: JN
# To disable starting forticlient after reboot:
# 1. Comment out the command (edit and add an `#` in front of the line) in file
#   `/opt/forticlient/start-fortitray-launcher.sh`
# 2. `sudo systemctl disable forticlient-scheduler`
# After step 1 and 2 above, forticlient daemon will not start after reboot. To

nylander

Recently, I tried to upgrade [nf-core](https://nf-co.re/) on my Ubuntu Linux but the execution after installation failed with errors from a python module.
Upgrading the python library ["rich"](https://rich.readthedocs.io/en/stable/introduction.html) solved the issue.

Steps below:

```
$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=20.04
DISTRIB_CODENAME=focal

nylander

#! /usr/bin/env perl
#
# Short description for fasta2nexus.pl
#
# Author nylander <[email protected]>
# Version 0.1
# Copyright (C) 2021 nylander <[email protected]>
# Modified On 2021-05-21 10:54
# Created  2021-05-21 10:54
#