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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

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#!/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, 

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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

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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,

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#!/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"

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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

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

@author: Ido Bar
"""

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// 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

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#!/bin/env perl

### david.studholme@tsl.ac.uk

### Generates contigs (in FastA) and scaffolding information (in AGP) from Velvet 'contigs.fa' supercontigs file

### Use entirely at you own risk!! There may be bugs!

### modified by chienchi@lanl.gov 2010/09/13
### add flags -i -size -o

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Setting up a cloud-based multi-user teaching server using conda

Setup steps

1. Apply for an allocation at NECTAR-RDS
2. Setup 2 key-pairs (one will be for 'root-designated' login and the other for 'general-user' login), download the private keys to a secure location. If you're planning to use KiTTY or PuTTY to login to the server from Windows, you'll need to convert the .pem key file to a .ppk, as explained here. You can (and should) password-protect this key (can be done in PuTTYgen when converting the key from the default .pem format to a PuTTY-supported .ppk).
3. Setup a customised security group to allow remote access (open port 22 for ssh logins and any addi