Build A MAC (Mavericks - OS X 10.9.5)

3) Update JAVA version to 1.7

Many of the tools you will use leverage JAVA and some need the 1.7 JDK to be available. To determine which version you have currently do the following

# Open a new terminal window

# Type the following

java -version

# Check to the version output

java version "1.6.0_65"

Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609)

Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)

Assuming you have not already update the java version for another reason you will need to download an updated version from Oracle. To download search google for "MAC Java Development Kit". I followed the "JAVA SE Development Kit 7 - Downloads | Oracle" link to download the "jdk-7u71-macosx-x64.dmg" file. To install, first accept the license at the top and click on the file to initiate the download. Once complete, click on the download, then click on the install package and follow the prompts. Then close all terminal windows and ensure the program is quit, then open a new window and check the version.

java -version

# The output should now indicate the updated 1.7 version is available as default

java version "1.7.0_71"

Java(TM) SE Runtime Environment (build 1.7.0_71-b14)

Java HotSpot(TM) 64-Bit Server VM (build 24.71-b01, mixed mode)

4) Install R

R is free software that supports a multitude of statistical and graphic applications. To download, search google for "R" and follow the links to a CRAN download page of your choosing.

Download by clicking the "Download R for (Mac) OS X" link to the pre-compiled binary. (current version is R-3.1.2, Pumpkin Helmet, 2014-10-31).

To install open the install package (R-3.1.2-mavericks.pkg) and follow the prompts.

Once installed open the application (Applications>R)

Then install the following using the Package Installer (Packages & Data > Package Installer).

NOTE: It is good habit to select the "Install Dependencies" radio button

CRAN (binaries)

ggplot2

mass

scales

gdata

gridExtra

Hmisc

vennDiagram, also (bvenn, colorfulVennPlot, eVenn, venneuler)

psych

PBSmapping

data.table

maptools

maps

Bioconductor (binaries)

DESeq

DESeq2

DNAcopy

5) Install Rstudio

Rstudio is a nice graphical interface for using R. It made it much less scary to use R for making graphs as you get instantaneous feed back. To download search google for "R studio" and follow the links to download the Open Source version of RStudio Desktop.

To install, click on the download (RStudio-0.98.1091.dmg) and drag the RStudio application to your applications folder.

6) Install/Update Python

Macs ship with python 2.7 but if you are starting out it is not a bad idea to update to python 3.x. To download the newer version google "python" and follow the links to download the "Mac OS X 64-bit/32-bit installer".

To install, click on the install package (python-3.4.2-macosx10.6.pkg).

NOTE/WARNING: Several essential Mac applications use python 2.7, so you need to leave it as default but you can easily use the 3.4 environment

Open the python interpreter in the terminal

python3

Exit the interpreter

exit()

In a script use the following header line

#!/usr/bin/env python3

OR CALL SCRIPT WITH

python3 YourSupperCoolScript.py

There are a number of very valuable packages you might want for scientific computing included in the scipy.org library such as numpy and pandas. They can be installed using pip as follows:

pip3.4 install numpy

pip3.4 install ipython

pip3.4 install scipy

pip3.4 install matplotlib

pip3.4 install sympy

pip3.4 install pandas

pip3 install jupyter

# samtools in python

pip3.4 install pysam

7) Install MacPorts

There are many unix commands that do not come pre-loaded on Macs like dos2unix, wget or md5sum. To install these and many other tools MacPorts is an excellent resource. To download, google "MacPorts" and follow the "Installing MacPorts" instructions for your OS version (Make sure Xcode is available).

To install, click on the download (MacPorts-2.3.3-10.9-Mavericks.pkg)

Test the install by opening a new terminal window and typing the following

port version

Assuming this produced the version not "command not found" you are ready to install needed ports as follows in a terminal window:

sudo port install wget

sudo port install dos2unix

sudo port install md5deep

sudo port install gawk

sudo port install cairo        ## Used to install Pairoscope

sudo port install doxygen ## Used to install Pairoscope

sudo port install cmake ## Used to install Pairoscope

8) Install IGV

Integrated Genomics Viewer (IGV), is the defacto standard for a light weight GUI application that allows you to visualize a multitude of genomic data formats. There are several version available on the IGV website (http://www.broadinstitute.org/igv/). We generally use the binary version as it can be configured for your exact system unlike the Java Web Start versions. The file can be downloaded through your web browser, but since we have now installed "wget" we will do it from the command line.

Right click on the binary download link (you may have to login first) and select "copy link address"

# Open a new terminal window

cd local

wget http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip    ## This was the version at time of writing

unzip IGV_2.3.40.zip

cd IGV_2.3.40

# Update the igv.command file to set Xmx2000m to the appropriate value for your system

# Xmx is the maximum amount of memory you will allow IGV to use, I typically recommend 50-75% of the available RAM

vim igv.command

exec java -Xmx4000m

# Now add an alias to your .profile so you can open IGV by typing IGV into the terminal

vim ~/.profile

# Add the following alias

alias IGV='$HOME/local/IGV_2.3.40/igv.command'

# Now to start IGV open a terminal window and type:

IGV

9) Install Sequence Analysis Tools

a) Samtools - This is the base toolset for most manipulations of sequence/binary alignment maps (SAM/BAM)

# Download the current version of from (www.htslib.org)

# Right click on the download and select "copy link address", then use wget in the terminal to download

# Open a new terminal window

cd local

# You might need to delete "/download" from the end of the link for proper function

wget http://sourceforge.net/projects/samtools/files/samtools/1.1/samtools-1.1.tar.bz2

# Uncompress the package

tar xvjf samtools-1.1.tar.bz2

# Build the application and add to you $PATH folder $HOME/local

cd samtools-1.1

make

make prefix=$HOME/local install

b) Bcftools - This package is part of the samtools distribution. It is required for variant calling with samtools

# Download the current version of from (www.htslib.org)

# Right click on the download and select "copy link address", then use wget in the terminal to download

cd ~/local

wget http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2

tar xvjf bcftools-1.1.tar.bz2

cd bcftools-1.1

make

make prefix=$HOME/local install

c) Htslib - This package is part of the samtools distribution and installing it will make tabix and bgzip available

# Download the current version of from (www.htslib.org)

# Right click on the download and select "copy link address", then use wget in the terminal to download

cd ~/local

wget http://sourceforge.net/projects/samtools/files/samtools/1.1/htslib-1.1.tar.bz2

tar xvjf htslib-1.1.tar.bz2

cd htslib-1.1

make

make prefix=$HOME/local install

d) BWA - This is likely the most heavily used and broadly supported next-generation sequencing aligner. To download search google for "bwa aligner" and follow the links to download the current version

# Right click on the download and select "copy link address", then use wget in the terminal to download

cd ~/local

wget http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.10.tar.bz2

tar xvjf bwa-0.7.10.tar.bz2

cd bwa-0.7.10

make

cp bwa ~/local/bin

e) Picard - This set of JAVA applications provides a series of essential tools required for a multitude of sequencing analysis steps. To download, search google for "picard tools" and follow the "Latest Download" link to download the current version

# Right click on the download and select "copy link address", then use wget in the terminal to download

cd ~/local

wget https://github.com/broadinstitute/picard/releases/download/1.125/picard-tools-1.125.zip

unzip picard-tools-1.125.zip

cd picard-tools-1.125

cp picard.jar ~/local/bin/

NOTE: This example version is dramatically different than previous versions as it adopts a GATK like command format as all the applications are embeded in a single .jar file as opposed to independent .jar files for each application seen in previous versions. Clearly this will only work with updated pipelines.

f) GATK - This JAVA application contains a number of "best-practices" applications for post-processing alignment files. It also has a large number of additional applications that you will use frequently. To download, search google for "GATK tools" and follow the download links. Since the Broad Institute has commercialized the toolset with Appistry you will need to first register/login to accept the usage agreement. If you are using it for non-commercial research purposes you can use the free version.

#Due to the license restrictions the only download mechanism is via your web browser. By default the file lands in your "Downloads" folder.

cd ~/Downloads

# To see the actual file name, and sort the file, should be most recent download to the bottom, so you can easily see it

ls -lhtr

mv GenomeAnalysisTK-3.3-0.tar.bz2 ~/local/

cd ~/local

tar xvjf GenomeAnalysisTK-3.3-0.tar.bz2

# For some reason they don't create a versioned subfolder, Argh...

mkdir GenomeAnalysisTK-3.3-0

mv GenomeAnalysisTK.jar GenomeAnalysisTK-3.3-0/

mv resources/ GenomeAnalysisTK-3.3-0/

cd GenomeAnalysisTK-3.3-0

cp GenomeAnalysisTK.jar ~/local/bin/

g) snpEff/snpSift - These are two very handy tools. snpEff will provide annotations for your genome of interest to any VCF file you create. snpSift, can be used to manipulate VCF files for filtering, selection, and conversion to flat files (excel, text.txt, etc....). To download, google "snpeff" and follow the links to download page (http://sourceforge.net/projects/snpeff/files/).

# Right click on the most recent download, I don't do the "latest" as I like to have the versioned download, then select "copy link address".

cd ~/local

wget http://sourceforge.net/projects/snpeff/files/snpEff_v4_0_core.zip

unzip snpEff_v4_0_core.zip

# The download is versioned but the unzipped folder is NOT, so change the folder name to include a version (MAKE SURE TO VERSION CORRECTLY)

mv snpEff snpEff-4.0

cd snpEff-4.0

cp *.jar ~/local/bin

# Now that you have them installed you will need to configure snpEff (we are assuming you are still in the snpEff folder)

# Open the config file and update the data.dir line from (data.dir = ./data/   TO   data.dir = ~/local/snpEff-4.0/data/)

vim snpEff.config

# Find the data.dir line and update it, this makes sure the data folders are connected to the version you are using.

data.dir = ~/local/snpEff-4.0/data/

# Now you are ready to download the appropriate database(s) for you work (we are assuming you are still in the snpEff folder)

# There a thousands of genome and annotation versions available, we use the GRCh37 reference with ensembl 74 annotations

# Check the snpEff website for additional instructions if needed

# WARNING - This can take a long time and there is no progress window so be patient!!

java -jar snpEff.jar download GRCh37.74

h) Circos - This tool is used to produce the fancy circular diagrams that show mutations, structural differences, and copy number differences. You can fine tune these plots to the nth degree. Unfortunately, this is one of the most difficult programs to get installed but the documentation is excellent making it well worth the effort. To download, google "circos plot" or follow the link to (circos.ca) and follow the links to download the core distribution and tools.

#Right click on the most recent core version and select "copy link address", then paste after wget in terminal to download

cd ~/local/

wget http://circos.ca/distribution/circos-0.67-3.tgz

tar xvzf circos-0.67-3.tgz

# Now for the fun part of getting everything setup...  I promise it works

cd circos-0.67-3/bin/

# Step1 - Update the "circos" file to point to the correct environment directory change (#!/bin/env perl  To  #!/usr/bin/env perl)

# make a backup copy

cat circos > OLD_circos

# Open the circos file to edit in vim

vim circos

# Change the first line to

#!/usr/bin/env perl

# Now that you have saved the updated version test to determine which required modules are not available

./circos -module

## This is the output that was produced on my machine

ok       1.26 Carp

missing            Clone

missing            Config::General

ok    3.39_02 Cwd

ok   2.135_06 Data::Dumper

ok       2.51 Digest::MD5

ok       2.84 File::Basename

ok    3.39_02 File::Spec::Functions

ok       0.22 File::Temp

ok       1.51 FindBin

missing            Font::TTF::Font

missing            GD

missing            GD::Polyline

ok       2.38 Getopt::Long

ok       1.16 IO::File

missing            List::MoreUtils

ok       1.25 List::Util

missing            Math::Bezier

ok      1.997 Math::BigFloat

missing            Math::Round

missing            Math::VecStat

ok       1.02 Memoize

ok       1.30 POSIX

missing            Params::Validate

ok       1.51 Pod::Usage

missing            Readonly

missing            Regexp::Common

missing            SVG

missing            Set::IntSpan

missing            Statistics::Basic

ok       2.34 Storable

ok       1.16 Sys::Hostname

ok       2.02 Text::Balanced

missing            Text::Format

ok       1.9725 Time::HiRes

## Now to work on installing all the missing modules using the CPAN downloader in the terminal

sudo perl -MCPAN -e shell

install GD

# You will be asked if you want to install dependancies as it goes, I answered "yes" to all of these queries

install Clone

install Config::General

install Font::TTF::Font

install List::MoreUtils

install Math::Bezier

install Math::Round

install Math::VecStat

install Params::Validate

install Readonly

install Regexp::Common

install SVG

install Set::IntSpan

install Statistics::Basic

install Text::Format

exit

## Now test if all the required modules are now available

./circos -module

# If all went well each and every module should now be marked as 'ok'

#Download the circos tools

cd ~/local/

wget http://circos.ca/distribution/circos-tools-0.20.tgz

tar xvzf circos-tools-0.20.tgz

#Download the tutorials and Test the Install

cd ~/local/

wget http://circos.ca/distribution/circos-tutorials-0.67.tgz

tar xvzf circos-tutorials-0.67.tgz

cd circos-tutorials-0.67/tutorials/2/2/

~/local/circos-0.67-3/bin/circos -conf circos.conf

You should see a series of messages print to the terminal screen. If you navigate to the folder using the finder window you should see a new file called "circos.png". Open the image file and check to ensure it produced a circular image of each human chromosome with each chromosome in a different color.

#To make it easier to use circos we will add an alias to our profile

# Open your profile and add an alias to the circos binary

vim ~/.profile

alias CIRCOS='$HOME/local/circos-0.67-3/bin/circos'

# Close the terminal application and reopen to test the alias function

cd circos-tutorials-0.67/tutorials/2/2/

CIRCOS -conf circos.conf

As our pipeline developer would say... "Much Success!!"

i) Pairoscope - This one was painful to sort out... yet again. But if you follow these instructions it should work well. To access the download you will use "git" but to see how we got to things you can access the Wash U tools website (http://tvap.genome.wustl.edu/tools/) and follow the links to the pairoscope download.

cd ~/local/

git clone https://github.com/genome/pairoscope.git

mkdir pairoscope/build

cd pairoscope/build

cmake ../

make -j

# If you get an error like I did doing this I can save you a day of effort if you follow these steps

cd vendor/src/gtest160/include/gtest/internal

# Now we need to edit the "gtest-port.h" file to change a 1 to a 0 in the middle of the file (I have no idea why this works but it does)

vim gtest-port.h

# You will need to edit line number 437 from  # define GTEST_HAS_TR1_TUPLE 1   TO    # define GTEST_HAS_TR1_TUPLE 0

# To view line numbers

:set nu

# To navigate straight to line 437

:437

# Enter edit mode by typing "i" and then edit the line so it looks like:

# define GTEST_HAS_TR1_TUPLE 0

# Save the changes, you might have to force the save after you exit edit mode by hitting <esc>

:w!

:q

# Okay now lets try it again

cd ~/local/pairoscope/build/

make -j

# Assuming that worked, now move the binary to the local/bin directory

cd bin

cp pairoscope ~/local/bin

j) FASTQC - This is an excellent program for visually checking the quality of your sequencing reads before alignment

cd ~/local/

wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.2.zip

unzip fastqc_v0.11.2.zip

cd FastQC

chmod +x fastqc

# Add a symbolic link to the $HOME/local/bin $PATH directory so you can call the application easily

ln -s ~/local/FastQC/fastqc ~/local/bin/fastqc

k) BedTools - This program is very useful for manipulating and counting

cd ~/local/

wget https://github.com/arq5x/bedtools2/releases/download/v2.22.0/bedtools-2.22.0.tar.gz

tar xvzf bedtools-2.22.0.tar.gz

cd bedtools2

make

cd bin

cp bedtools ~/local/bin

l) SeqTK - This program allows you to manipulate fasta and fastq files

cd ~/local/

git clone https://github.com/lh3/seqtk.git

cd seqtk

make

cp seqtk ~/local/bin

1. Bowtie
2. Tophat
3. STAR
4. HT-Seq
5. FeatureCounts
6. Sailfish
7. FASTX
8. SAMBLASTER (LINUX ONLY?)