Ido Bar IdoBar

set -e, -u, -o, -x pipefail

The set lines

These lines deliberately cause your script to fail. Wait, what? Believe me, this is a good thing.
With these settings, certain common errors will cause the script to immediately fail, explicitly and loudly. Otherwise, you can get hidden bugs that are discovered only when they blow up in production.

set -euxo pipefail is short for:

set -e
set -u

Bash best practices and style-guide

Just simple methods to keep the code clean.

Inspired by progrium/bashstyle and Kfir Lavi post.

Quick big rules

All code goes in a function
Always double quote variables

Introduction

The following code snippets demonstrate an approach to substantially speed-up BLAST searches of large query files (whole transcriptomes/genomes) that are performed against the NCBI nr/nt/refseq databases by running small jobs annotating subsets of the input sequences against subsets of the databases.
The method is based on "divide and conquer" approaches [1–2] that split the search query and the database to multiple small jobs that require modest resources and time which can utilise high priority queues and are therefore ideal for an HPC setting. The exact number of jobs to be submitted is dependant on the specifics of the HPC cluster, primarily number of available nodes, queues limits and system loads and therefore need to be experimented for optimal results.

Requirements

The suggested script is tailored to run on the QRIS Awoonga HPC cluster, using [Conda environment](https://docs.conda.io/en/latest

	#! /bin/bash

	## See also https://github.com/nextflow-io/nextflow/discussions/4308

	## cd to a parent directory for a Nextflow pipeline executation, i.e. contains .nextflow and work directories
	WORKDIR=$1
	## Find work directories essential to the last pipeline run, as absolute paths
	nextflow log last > $WORKDIR/preserve_dirs.txt

	## Find all work directories, as absolute paths

	#!/bin/bash

	if [ $# -ne 1 ]; then
	echo "Usage: $0 <input_gtf_file>"
	exit 1
	fi

	input_gtf="$1"
	output_prefix="output"
	sorted_gtf="${output_prefix}.sorted.gtf"

	#!/usr/bin/env Rscript
	#PBS -V

	# This script will call copy number variants using cn.mops
	# usage: Rscript cn.mops.R --help

	library(optparse)

	option_list = list(
	make_option(c("-i", "--input_dir"), type="character", default=NULL,

	stat_smooth_func <- function(mapping = NULL, data = NULL,
	geom = "smooth", position = "identity",
	...,
	method = "auto",
	formula = y ~ x,
	# show_formula = TRUE,
	se = TRUE,
	n = 80,
	span = 0.75,
	fullrange = FALSE,

	#!/bin/bash
	# put this file in $HOME/bin and make it executable
	# make sure that this file is being called by default, I did this by adding `alias "qstat=~/bin/qstat"` to my ~/.bashrc

	# Servers
	#awoonga="@awongmgmr1.storage:16001 @awonmgr2.storage:16001"
	#flashlite="@flm1.ipoib:16001 @flashmgr2.ipoib:16001"
	#tinaroo="@tinmgmr1.ib0:16001 @tinmgr2.ib0:16001"
	awoonga="@awonmgr2"
	flashlite="@flashmgr2"



	# -- coding: utf-8 --
	"""
	Created on Tue Jan 28 16:34:57 2020

	@author: Ido Bar
	"""

	// See these instruction to enable js scripting in Zotero:
	// https://forums.zotero.org/discussion/comment/324734/#Comment_324734
	var fieldName = "title";
	var plantsPathogens = ["Cryptobranchus", "Fusarium", "Mycosphaerella", "Pochonia", "Pogona", "Nannizziopsis", "Armillaria", "Parastagonospora", "Pseudoperonospora", "Phytophthora", "Heterobasidion", "Cochliobolus", "Rhynchosporium", "Aspergillus", "Ascochyta", "Sclerotinia", "Botrytis", "Cicer", "Lens","Oryza", "Eucalyptus", "Arabidopsis", "Vigna", "Phaseolus", "Vicia"];
	var aquaticSpecies = ["Oreochromis", "Dicentrarchus", "Pagrus", "Gonostoma","Tursiops", "Gadus", "Danio", "Acanthosentis", "Oryzias", "Seriola", "Cyprinus", "Euthynnus", "Solea", "Nibea", "Thunnus thynnus","Argyrosomus", "Thunnus", "Misgurnus", "Oncorhynchus", "Epinephelus", "Rachycentron", "Clarias", "Tetraodon", "Proterocara", "Latimeria", "Oithona", "Sarda", "Glaucosoma", "Scomberomorus", "Allium", "Aulopus", "Plecoglossus", "Anguilla", "Hoplias", "Poecilia", "Sardinops", "Cyprinus", "A