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 <johan.nylander@nrm.se>
# Version 0.1
# Copyright (C) 2021 nylander <johan.nylander@nrm.se>
# Modified On 2021-05-21 10:54
# Created  2021-05-21 10:54
#

nylander

#!/bin/bash

# ptemplate - Create a project structure
# Usage: ptemplate myproject
# Last modified: Mon mar 29, 2021  07:55
# Sign: Johan Nylander
# Description: Create a folder structure
# and, if git is available, initilize git-
# version control. No files in folder private
# is under git control, and only the README file

nylander

8 484
Barbotinia_oraniensis         TCTTGGTCCATTTATATGTGAGATATATGCAATGCTTGGCTCCCTATTTGGATGTGGCTCCATTTGGACAATGTGTATGATTGCTTTCGACCGATACAATGTTATCGTAAAAGGTTTAGCTGGCAAGCCATTAACTATCAGTGGTGCAATTCTGCGTATTGTTTTTCTCTGGGTCTGGGCGGTAGTTTGGACCATTGCACCAATGATAGGATGGAATCGG---TACGTTCCCGAGGGCAACATGACAGCTTGTGGAACTGACTATCTAACTAAGGATTGGTTCTCGAGGTCTTACATTCTTGTATACAGCGTCTTCGTATACTTCATGCCACTTTTCCTCATCATCTACAGTTACTATTTCATCATTGCTGCTGTATCTGCTCATGAAAAAGCTATGCGTGAACAGGCCAAAAAGAWGAATGTAGCTTCTCTACGATCATCCGACAATCAAAATACGAGTGCTGAACATAAACTCGCCAAGGCA
Synergus_gallaepomiformis     ACTAGGTCCATTTATATGTGAGATGTACGGAATGTTTGGCTCTCTATTCGGATGTGGTTCTATTTGGACAATGTGTATGATTGCTTTCGACCGATACAACGTTATCGTAAAAGGTTTAGTTGGCAAGCCCTTAACTATCAGTGGTGCAATCCTGCGCATTGCTTTTCTCTGGATCTGGGCAGTAATTTGGACAATCGCACCAATGATAGGATGGAATCGG---TACGTTCCGGAGGGTAACATGACAGCTTGCGGAACTGACTACCTGAGTAAGGATTGGTTCTCCAGGTCTTACATCATTGTATACAGCGTCTTTGTATACTTCATGCCACTTTTCCTCATCATATACAGTTACTACTTCATCATTGCTGCTGTATCTGCCCACGAGAAGGCTATGCGTGAACAGGCCAAAAAGATGAATGTAGCTTCTCTACGATCATCCGACAATCAAAATACGAGTGCTGAACATAAAC

nylander

# Bash alias for better jobinfo output on UPPMAX.
# Last modified: 2020-05-27
# Sign: Johan Nylander
# Include in your ~/.bash_aliases, and
# check that your ~/.bashrc reads your ~/.bash_aliases by, e.g.,
# including this in your ~/.bashrc:
#    if [ -f ~/.bash_aliases ]; then
#      . ~/.bash_aliases
#    fi
#

nylander

#NEXUS
[Data from Table 1, Felsenstein, 1992, Evolution, 46(1),1992, pp. 159-173.]
Begin data;
  Dimensions ntax=5 nchar=122;
  Format datatype=restriction missing=?;
  Matrix
    Gibbon  11100000110001000010100111100000011100100100111110000001010001100100000000010000011010100111100011011010111111101101011001
    Orang   11010110100111000000011000101010010000010101010010001000101000000011000000000010000111001110001000110011101001000111001110
    Gorilla 11000101101001010111000001100001110011000000000010100000110100110001011000101011000010000101110000110000101101010110101000
    Chimp   10000110100011111010000001000100110010101000000011000111100010110000100110000011100010001101100000110100001001010110111000

nylander

# gh-93: Repository surgery: Remove large files accidentally added in the past.

- Last modified: fre aug 09, 2019  12:34
- Sign: JN

## Description

Find large, unnecessary files in the MrBayes GitHub repository and delete them.
Saves approx. 132 MB of space (from 212 to 80 MB).