IdoBar

# Run this script in a directory containing zip files from fastqc. It aggregates images of each type in individual folders
# So looking across data is quick.

zips=`ls *.zip`

for i in $zips; do
    unzip -o $i &>/dev/null;
done

fastq_folders=${zips/.zip/}

IdoBar

Windows Registry Editor Version 5.00 

[HKEY_CURRENT_USER\Software\SimonTatham\PuTTY\Sessions\Default%20Settings]
"Colour0"="217,230,242"
"Colour1"="217,230,242"
"Colour2"="14,27,48"
"Colour3"="14,27,48"
"Colour4"="14,27,48"
"Colour5"="217,230,242"
"Colour6"="0,0,0"

IdoBar

#! /bin/bash
# Ask user for sudo password (to be used when needed)
read -s -p "Enter Password for sudo: " sudoPW

# update CRAN repository below if needed
REPO="'https://cran.rstudio.com/'"

# Based on the instructions on Dean Attali's website:
# https://deanattali.com/2015/05/09/setup-rstudio-shiny-server-digital-ocean/#user-libraries

IdoBar

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

IdoBar

#!/bin/env perl

### [email protected]

### 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 [email protected] 2010/09/13
### add flags -i -size -o

IdoBar

// 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

IdoBar

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

@author: Ido Bar
"""

IdoBar

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

IdoBar

#!/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"

IdoBar

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,