mojaveazure

#!/bin/bash

set -e
set -u
set -o pipefail

#   A script to subsample Fasta/FastQ files using Seqtk
if ! `command -v seqtk > /dev/null 2> /dev/null`
then
    echo "Failed to find seqtk!"

mojaveazure

#!/bin/bash

set -e
set -u
set -o pipefail

if ! `command -v fastq-dump > /dev/null 2> /dev/null`
then
    echo "Can't find fastq-dump!"
    exit 1

mojaveazure

#!/bin/bash

set -e
set -o pipefail

###########################################################################################################################
#########################################           Usage Information             #########################################
#   This is a script to extract adapter sequences that use barcodes embedded in the names of files
#   To use, add a list of samples to the SAMPLE_INFO field on line 34
#       This should look like:

mojaveazure

#!/bin/bash

#   A function that checks the extension of a file
function checkExtension() {
    FILE="$1"
    EXTENSION="$2"
    if [[ "${FILE: -4}" == "${EXTENSION}" ]]
    then
        echo yes
        return 0

mojaveazure

#!/usr/bin/env python

import argparse

parser = argparse.ArgumentParser(add_help=True, description="A switch argument in Python")

parser.add_argument('-s',
    '--switch',
    help="The switch",
    action='store_true',

mojaveazure

#!/bin/bash

#	This script downloads and installs SAMTools
#	The current version of SAMTools is v1.3

set -e
set -o pipefail

#	What versions of SAMTools are we downloading?
SAMTOOLS_VERSION="1.3"

mojaveazure

R Formula Specifications

Adapted from the National Park Service

---

Right-Side

Right Side	Meaning
A + B	Main effects of A and B
A:B	Interaction of A with B

mojaveazure

#!/bin/bash

set -e
set -o pipefail

#   Extract regions from a BED file and format it for use with ANGSD and ANGSD-wrapper

function Usage() {
    echo -e "\
Usage:  $(basename $0) BED_FILE NUMBER [OUTFILE] [SEED] \n\

mojaveazure

#!/bin/bash

#   This script is designed to install Platypus on MSI

set -e
set -o pipefail

INSTALL_DIR=${1:-$(pwd)}

echo "Installing Platypus into ${INSTALL_DIR}..." >&2

mojaveazure

#!/bin/bash

set -e
set -o pipefail

#   Check for dependent programs
if ! `command -v samtools > /dev/null 2> /dev/null`; then echo "Please install SAMTools and place in your PATH"; exit 1; fi # Do we have SAMTools installed?
if ! `command -v bcftools > /dev/null 2> /dev/null`; then echo "Please install BCFTools and place in your PATH"; exit 1; fi # Do we have BCFTools installed?

#   Create a usage message