sbamin

#!/usr/bin/env bash

## Convert PDF to PDF/A
## requires imagemagick and ghostscript 
## Main script by Rob Patro
## https://gist.github.com/rob-p/9f52c9722fe65cae6946705babc7cddb

set -euo pipefail

pn="$1"

sbamin

This gist I write, because I couldn't find step by step instructions 
how to install and start postgresql locally and not globally in the
operating system (which would require sudo).

I hope, this will help especially people new to postgresql!

####################################
# create conda environment
####################################

sbamin

PBJelly gapclosing

PBJelly is a part of the PBSuite package of programs. PBJelly can be used to try to close or shrink gaps that may be present between contigs after scaffolding.

The official documentation is availible at: http://sourceforge.net/p/pb-jelly/wiki/Home/

Most of PBJelly can be configured through an .xml protocol that you have to create with a text editor. It is best to put this in the directory where your output is going. Below is an example of how this xml protocol can look:

<jellyProtocol>

/path/to/reference.fasta

sbamin

gzip compression to save disk space

• find file types ending .txt, .fq, or .fastq with > 500 MB size; compress using .gz and replace file in-place.

• better to run script as slurm job.

• list files and save output.

useful to uncompress at the later date - avoid file extension of log file matching that of find query else .<ext> will get replaced by .<ext>.gz

sbamin

{
	http_port 80
	https_port 443
	# auto_https off
	# debug
}

avocado.example.com {
  	root * /srv

sbamin

#!/bin/bash

## Script to run immediately after any sbatch job begins
## Throttle disk I/O if fastscratch is near 100 %
## @sbamin

## execute prior to running each of snakemake job
tmpjobstart="$(date +%d%b%y_%H%M%S_%Z)"

echo "${tmpjobstart}: Running slurm prerun.sh on HPC SUMNER"

sbamin

The fastest remote directory rsync over ssh archival I can muster (40MB/s over 1gb NICs)

This creates an archive that does the following:

rsync (Everyone seems to like -z, but it is much slower for me)

• a: archive mode - rescursive, preserves owner, preserves permissions, preserves modification times, preserves group, copies symlinks as symlinks, preserves device files.
• H: preserves hard-links
• A: preserves ACLs

sbamin

--[[
## Modulefile in lua syntax
## Author: Samir Amin

## Read about Lmod
## https://lmod.readthedocs.io/en/latest/015_writing_modules.html
## https://lmod.readthedocs.io/en/latest/050_lua_modulefiles.html
## https://lmod.readthedocs.io/en/latest/020_advanced.html
--]]

sbamin

#!/bin/bash

## Use NIH RePORTER API to fetch grant records
## @sbamin

# usage
show_help() {
cat << EOF

Use NIH RePORTER API to fetch grant records.

sbamin

#!/bin/bash
#SBATCH --job-name=crons_q2days                        # name of the job
#SBATCH --chdir=/home/user/logs/crons                             # the workding dir for each job
#SBATCH --output=/home/user/logs/crons/log_crons_q2days.out                           # output is sent to logfile, stdout + stderr by default
#SBATCH --error=/home/user/logs/crons/log_crons_q2days.err                            # output is sent to logfile, stdout + stderr by default
#SBATCH --qos=batch                               # Job queue
#SBATCH --time=00:10:00                      	 # Walltime in minutes
#SBATCH --mem=2G                              # Memory requirements in Kbytes
#SBATCH --nodes=1                 		     # Nodes reserved
#SBATCH --ntasks=1                 			 # CPU reserved