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# Load GO and DE data to R

## @knitr prep_data

# Install missing CRAN packages if needed

# git.packages <- c("docopt/docopt.R")
# github.packages <- c("argparser")
install.deps <- function(p, repo="cran"){
  call_install <- switch(repo,cran=c("install.packages(package, repos=\"http://cloud.r-project.org/\""),

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#' call primer3 for a given set of DNAstringSet object
#' Forked from https://gist.github.com/al2na/8540391
#' TODO: Add support for target amplicon region (Maybe as [] in the fasta input)
#' @param seq: DNA template as a character string (required)
#' @param fw_primer: optional forward (left) primer, if provided Primer3 will assess it and will try to find a suitable reverse primer. Default: NULL
#' @param rv_primer: optional reverse (right) primer (must be reverse-complemented to the template), if provided Primer3 will assess it and will try to find a suitable forward primer. Default: NULL
#' @param size_range: a string with space separated list of desired amplicon size ranges. Default: '151-500'
#' @param Tm: range of melting temprature parameters as a numerical vector containing (min,optimal,max). default: c(55,57,58)
#' @param name: name of the amplicon in 'chr_start_end' format
#' @param sequence_target: a string containing space separated list of target pairs: 'starting_position,target_length starting_p

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$path = $args[0]

[Reflection.Assembly]::LoadWithPartialName("System.Windows.Forms"); 
$i = new-object System.Drawing.Bitmap $path

$i.RotateFlip("Rotate90FlipNone")

$i.Save($args[1],"png")

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#!/bin/bash -v

# Define these according to the run
N=5000
NCPUS=4
# Use wildcards or specify an exact input fasta filename below (should be in your current working directory)
INPUT_FASTA="input.fasta"
DATE=`date +%d_%m_%Y`
REFDB="nt"
#CMD=`printf "hmmscan --cpu %s --domtblout \%s/\%s.pfam.domtblout ~/.hmmer-3.1/Pfam/Pfam-A.hmm \%s > \%s/\%s_pfam.log",$NCPUS`

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#!/bin/bash

# installs plenv, perl, carton, cpanminus, sets up environment in .bash_profile or .profile
# from https://github.com/tokuhirom/plenv#readme
MY_PROFILE_FILE="$HOME/.profile"

if [[ -n "$PERL_MB_OPT" ]]; then
    echo "You must unset your local::lib environment variables first"
    echo "Edit your ~/.bash_profile or ~/.bashrc and remove any references"
    echo "to local::lib or export PERL*..."

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# util.R:
# Utilities to make R a happier place
# Originally created by Brendan O'Connor, brenocon.com/code
# Edited by Ido Bar.
# Source the file directly from this gist using `devtools::source_gist("7f63547158ecdbacf31b54a58af0d1cc", filename = "util.R")`


########################################
## Put everything into an environment, to not pollute global namespace

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# If loading in an environment that doesn't respect my RPATH environment
# variable, set it here
sourceDir <- file.path(path.expand("~"), "R", "source")
if (Sys.getenv("RPATH") == "") {
	if (!file.exists(sourceDir)) dir.create(sourceDir)
	Sys.setenv(RPATH=sourceDir)
}

# Load commonly used functions and packages

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#!/bin/bash

_usage() {
cat <<EOF
$*
        Usage: $0 <[options]>
        Options:
                 -i --in       input fasta file. If not specified will defaults to stdin [-]
                 -o --out      output combined results file. If not specified will defaults to stdout [-]
                 -p --parts    how many parts to break to input fasta into [default:5000]

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Setting up a new computer for scientific and bioinformatics data analysis

Follow these instructions to setup a new computer with commonly used tools and software for scientific data analysis (with emphasis on bioinformatics)

Windows machine

Use https://ninite.com/ to install the following open source software:

1. FileZilla - FTP file transfer
2. Firefox - web browser, add cliget addon for easy curl/wget download links
3. PuTTY - remote shell access
4. Java 8
5. .NET - framework needed for Paint.net

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Goal

• To create UniRef90 protein databases for NCBI blast and Diamond Blast
• To create a tab delimited taxid mapping file with two columns : sequenceID\tNCBITaxonID

Steps:

Download the uniref90 xml file first (warning - this is ~15 GB, will take a while)