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MoVRs - system wide installation of required software

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README

Sources and installation notes (current as of August 19, 2016)

Our recommendation is to install the required programs system-wide. Typical would be to run the installation steps as superuser after "cd /usr/local/src". Even better might be to create a directory /usr/local/src/MoVRs and install the programs there; this might avoid clashes with other programs you are running that possibly depend on earlier versions of the same packages.

Sources of the programs are listed. Please see the cited URLs for details on the software and installation.

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BLAST

	mkdir BLAST; cd BLAST
	wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.9.0+-x64-linux.tar.gz
	tar -xzf ncbi-blast-2.9.0+-x64-linux.tar.gz
	cd ncbi-blast-2.9.0+/bin
	cp * /usr/local/bin/
	cd ../../..

BLAT from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/

	mkdir BLAT
	cd BLAT
	wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat
	cp blat /usr/local/bin
	chmod a+x /usr/local/bin/blat
	cd ..

GHOSTSCRIPT from http://www.ghostscript.com/download/gsdnld.html

	mkdir GHOSTSCRIPT
	cd GHOSTSCRIPT
	wget https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs927/ghostscript-9.27-linux-x86_64.tgz
	tar -xzf ghostscript-9.27-linux-x86_64.tgz
	cd ghostscript-9.27-linux-x86_64
	cp gs-927-linux_x86_64 /usr/local/bin/gs
	cd ../..

MEME from http://meme-suite.org/doc/download.html

	mkdir MEME
	cd MEME
	wget http://meme-suite.org/meme-software/5.0.5/meme-5.0.5.tar.gz
	tar -xzf meme-5.0.5.tar.gz
	cd meme-5.0.5
	./configure --prefix=/usr/local/src/MEME/meme-5.0.5 --with-url="http://meme-suite.org"
	make
	make test
	make install
	cd ../..

SAMTOOLS

	mkdir SAMTOOLS
	cd SAMTOOLS
	git clone git://github.com/samtools/htslib.git htslib
	cd htslib
	make
	cd ..
	git clone git://github.com/samtools/samtools.git samtools
	cd samtools
	make
	cp samtools /usr/local/bin
	cd ../..

WEBLOGO from http://weblogo.berkeley.edu/

	mkdir WEBLOGO
	cd WEBLOGO
	wget http://weblogo.berkeley.edu/release/weblogo.2.8.2.tar.gz
	tar -xzf weblogo.2.8.2.tar.gz
	cd ..

HOMER from http://homer.salk.edu/homer/

	mkdir HOMER
	cd HOMER
	wget http://homer.ucsd.edu/homer/configureHomer.pl
	perl configureHomer.pl -install homer >& err
	chmod -R a+w data
	cd ..

MoVRs

	git clone https://github.com/BrendelGroup/MoVRs.git

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Setting up required R packages (execute the following within R):

	if (!requireNamespace("BiocManager", quietly=TRUE))
	   install.packages("BiocManager")
	BiocManager::install(c("seqLogo"))

Setting up your environment: bash

Add to ~/.bashrc the following lines (edit appropriately):

# needed for MoVRs:
#
export PATH="~/anaconda3/condabin:$PATH"
export PATH="$PATH:/usr/local/src/MoVRs/WEBLOGO/weblogo"
export PATH="$PATH:/usr/local/src/MoVRs/MEME/meme-5.0.5/bin"
export PATH="$PATH:/usr/local/src/MoVRs/HOMER/bin"
export PATH="$PATH:/usr/local/src/MoVRs/MoVRs/scripts"

Setting up your environment: python

There are different ways to do this. Here is one convenient and widely used way using Anaconda (as non-privileged user rather than root):

from https://www.continuum.io/downloads#_unix

	wget https://repo.anaconda.com/archive/Anaconda3-2019.07-Linux-x86_64.sh
	bash Anaconda3-2019.07-Linux-x86_64.sh 

Then you can create a python environment for MoVRs as follows:

conda create --name movrs python=3.6 networkx matplotlib
source activate movrs