janxkoci

#!/bin/bash
# bash strict mode
# http://redsymbol.net/articles/unofficial-bash-strict-mode/
set -euo pipefail
IFS=$'\n\t'

janxkoci

#!/usr/bin/awk -f

## gawk -i inplace -f update_scripts.awk scripts*.r

## some scripts define output variable without spaces
/^my_variable=/ && NF == 1 {
	split($0, myvar, "=")
	$1 = myvar[1]
	$2 = "="
	$3 = myvar[2]

janxkoci

janxkoci

#!/bin/bash

cd $PBS_O_WORKDIR || exit
source /storage/brno2/home/$USER/.bashrc

module add plink/2.0

## example: https://stackoverflow.com/a/17316302/5184574
# dowork() { 
#   echo "Starting i=$1, j=$2"

janxkoci

name: grass
channels:
  - conda-forge
dependencies:
  - proj
  - gdal
  - parallel # for parallelization
  - flex
  - bison # yacc parser
  - pdal

janxkoci

AWK(1)                                         General Commands Manual                                         AWK(1)

awk

NAME
       awk - pattern-directed scanning and processing language

SYNOPSIS
       awk [ -F fs ] [ -v var=value ] [ 'prog' | -f progfile ] [ file ...  ]

janxkoci

--- dropbox.py
+++ dropbox.py
@@ -134,11 +134,12 @@
         FatalVisibleError("Platform not supported")

 def is_dropbox_running():
-    pidfile = os.path.expanduser("~/.dropbox/dropbox.pid")
-
     try:
-        with open(pidfile, "r") as f:

janxkoci

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

janxkoci

#!/usr/bin/awk -f

function usage()
{
	print "Convert legofit model with estimates to slendr simulation script." > "/dev/stderr"
	print "usage: estlgo2slendr.awk model.lgo" > "/dev/stderr"
	err_exit = 1
	exit 1
}

janxkoci

#!/bin/bash
#PBS -l select=1:ncpus=64:mem=1gb,walltime=24:00:00

## GO TO WORKDIR
cd $PBS_O_WORKDIR || exit

## EXPORT PATH
export PATH="/storage/brno2/home/jena/bin:$PATH"
export PATH="/storage/brno2/home/jena/miniconda3/bin:$PATH"