################################################################################
	#                                                                              #
	# Copyright 2017 Megaprobe-Lab                                                 #
	#                                                                              #
	# This is software created by the megaprobe lab under the GPL3 license.        #
	#                                                                              #
	# This program reproduces the pipeline for de novo rna sequencing research. To #
	# run the program, just move into the folder that contains the Snakefile and   #
	# make sure the PATH has addeded Trinity, khmer, screed and                    #
	# sourmash. For more explanation on what the program does read technical       #
	# report or to see usage read the README.md                                    #
	#                                                                              #
	# Then utilize the command: "snakemake" to run the desired operation.          #
	################################################################################

Programs:

• Environment and khmer: http://khmer.readthedocs.io/en/v1.0.1/install.html
• Trinity: https://github.com/trinityrnaseq/trinityrnaseq/releases, https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity (v2.4)
• Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic (v0.36)
• Sourmash: https://sourmash.readthedocs.io/en/latest/tutorials.html#installing-sourmash
• Screed: https://pypi.python.org/pypi/screed
• Biopython: https://anaconda.org/anaconda/biopython
• Anaconda: https://anaconda.org/
• Snakemake: https://snakemake.readthedocs.io/en/stable/getting_started/installation.html

App requirments:

• Java-1.8 (or higher) : sudo apt-get install default-jre
• gcc greater than 4.3: sudo apt-get install gcc
• zlib: sudo apt-get install zlib1g-dev
• bowtie2: sudo apt-get install bowtie2 or http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Pip requirments:

• pip install PyYAML
• pip install screed
• pip install khmer or with conda install --name (name of enviorment) -c bioconda khmer=2.1
• pip install biopython
• pip install snakemake

Export Programs to Path:

• Like so: PATH=$PATH:~/path/to/file
• Trimmomatic
• Trinity
• Sourmash
• Screed

Modify Config.yaml

• Add working directory
• Add path to Organisms
• Add Comparison like so: "0 1" This is Organisms 1 and 2.

Run the snakemake

• Have the Snakefile and config.yaml in the working directory
• run like so snakemake
• or snakemake
• for other uses use snakemake -h

Command to see how many sequences:

• grep -o 'TRINITY_DN' Trinity_Organism0.fasta-in-Trinity_Organism1.fasta.txt | wc -l