Build a MAC (Mojave - macOS 10.14.5)

mkdir -p local/bin

vim .profile

# This ensures when a vim window closes the edited text disappears

export TERM=xterm

############### 

## Define PATH locations 

###############

export PATH=$HOME/local/bin:$PATH

###############

## Configure Window Naming Function

###############

#Window Naming Function

function winname {

    printf "\e]2;$1\a"

    }

#Tab Naming Function

function tabname {

    printf "\e]1;$1\a"

    }

###############

## Alias

###############

# This alias allows you to type "ll" in the terminal to execute "ls -lh"

alias ll='ls -lh'

# Remote connections

# These alias's are examples that open connections to a computation resource (standard or ftp connections shown)

alias computer='ssh jkeats@computer.tgen.org'

alias cftp='sftp jkeats@computer.tgen.org' 

# Tidyverse (this adds most of the common tools/applications)

> install.packages("tidyverse")

  also installing the dependencies ‘colorspace’, ‘sys’, ‘ps’, ‘highr’, ‘markdown’, ‘xfun’, ‘zeallot’, ‘labeling’, ‘munsell’, ‘RColorBrewer’, ‘askpass’, ‘rematch’, ‘prettyunits’, ‘processx’, ‘knitr’, ‘yaml’, ‘htmltools’, ‘evaluate’, ‘base64enc’, ‘tinytex’, ‘utf8’, ‘vctrs’, ‘backports’, ‘generics’, ‘reshape2’, ‘assertthat’, ‘glue’, ‘pkgconfig’, ‘R6’, ‘Rcpp’, ‘tidyselect’, ‘BH’, ‘plogr’, ‘DBI’, ‘ellipsis’, ‘digest’, ‘gtable’, ‘lazyeval’, ‘plyr’, ‘scales’, ‘viridisLite’, ‘withr’, ‘curl’, ‘mime’, ‘openssl’, ‘clipr’, ‘cellranger’, ‘progress’, ‘callr’, ‘fs’, ‘rmarkdown’, ‘whisker’, ‘selectr’, ‘stringi’, ‘fansi’, ‘pillar’, ‘broom’, ‘cli’, ‘crayon’, ‘dplyr’, ‘dbplyr’, ‘forcats’, ‘ggplot2’, ‘haven’, ‘hms’, ‘httr’, ‘jsonlite’, ‘lubridate’, ‘magrittr’, ‘modelr’, ‘purrr’, ‘readr’, ‘readxl’, ‘reprex’, ‘rlang’, ‘rstudioapi’, ‘rvest’, ‘stringr’, ‘tibble’, ‘tidyr’, ‘xml2’

# Cowplot (formatting for ggplot outputs and panels, yes its a love/hate thing)

> install.packages("cowplot")

# gridExtra

> install.packages("gridExtra")

# gdata

> install.packages("gdata")

  also installing the dependency ‘gtools’

# data.table

> install.packages("data.table")

# maptools

> install.packages("maptools")

  also installing the dependency ‘sp’

# maps

> install.packages("maps")

# PBSmapping

> install.packages("PBSmapping")

# psych (provides a geometric mean method)

> install.packages("psych")

  also installing the dependency ‘mnormt’

# Hmisc

> install.packages("Hmisc")

  also installing the dependencies ‘checkmate’, ‘htmlwidgets’, ‘Formula’, ‘latticeExtra’, ‘acepack’, ‘htmlTable’, ‘viridis’

# TOOLS FOR MAKING VENN DIAGRAMS

> install.packages("VennDiagram")

  also installing the dependencies ‘formatR’, ‘lambda.r’, ‘futile.options’, ‘futile.logger’

> install.packages("bvenn")

> install.packages("colorfulVennPlot")

> install.packages("venn")

> install.packages("venneuler")

  also installing the dependency ‘rJava’

> install.packages("UpSetR")

# TOOLS FOR SURVIVAL ANALYSIS

> install.packages("survival")

> install.packages("survminer")

  also installing the dependencies ‘ggrepel’, ‘ggsci’, ‘ggsignif’, ‘polynom’, ‘exactRankTests’, ‘mvtnorm’, ‘KMsurv’, ‘zoo’, ‘km.ci’, ‘xtable’, ‘ggpubr’, ‘maxstat’, ‘survMisc’, ‘cmprsk’

# Tools for Single Cell Analysis

> install.packages('Seurat')

  also installing the dependencies ‘httpuv’, ‘sourcetools’, ‘bitops’, ‘lsei’, ‘bibtex’, ‘gbRd’, ‘shiny’, ‘later’, ‘caTools’, ‘R.oo’, ‘R.methodsS3’, ‘npsurv’, ‘globals’, ‘listenv’, ‘Rdpack’, ‘hexbin’, ‘crosstalk’, ‘promises’, ‘gplots’, ‘R.utils’, ‘ape’, ‘fitdistrplus’, ‘future’, ‘future.apply’, ‘ggridges’, ‘ica’, ‘igraph’, ‘irlba’, ‘lmtest’, ‘metap’, ‘pbapply’, ‘plotly’, ‘png’, ‘RANN’, ‘reticulate’, ‘ROCR’, ‘rsvd’, ‘Rtsne’, ‘sctransform’, ‘SDMTools’, ‘tsne’, ‘RcppEigen’, ‘RcppProgress’

# INSTALL BIOCONDUCTOR TOOLS

> install.packages("BiocManager")

> BiocManager::install("DESeq")

> BiocManager::install("DESeq2")

> BiocManager::install("GenomeInfoDb")

> BiocManager::install("DNAcopy")

### Open a Fresh Terminal Window

# Create a folder for GitHub Repositories

mkdir -p local/git_repositories

# Move into the created folder

cd local/git_repositories

#Download the solarized package

git clone git://github.com/altercation/solarized.git

#Enter the downloaded package, make the required directory and copy the color scheme

cd solarized/vim-colors-solarized/colors

mkdir -p ~/.vim/colors

cp solarized.vim ~/.vim/colors/

## This will ensure the VIM text editor will use the solarized format

vim ~/.vimrc

#Add the following lines (see VIM section on how to use vim)

syntax enable

set background=dark

colorscheme solarized

## This will ensure the Terminal will use the solarized format when you use the unix "ls" command

vim ~/.profile

#Add the following line to your profile

export CLICOLOR=1

python3

exit()

#!/usr/bin/env python3

OR CALL SCRIPT WITH

python3 YourSupperCoolScript.py

pip3 install --upgrade pip

pip3 install numpy (version 1.16.3)

pip3 install ipython (version 7.5.0)

pip3 install scipy (version 1.3.0)

pip3 install matplotlib (version 3.0.3)

pip3 install sympy (version 1.4)

pip3 install pandas (version 0.24.2)

pip3 install jupyter (version 1.0.0)

pip3 install pysam (version 0.15.2)  # Samtools in python

pip3 install pyvcf (version 0.6.8)   # VCF manipulation in python

port version

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

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

#Install required tools that are not available from macports

brew install pkg-config       ## Needed to install perl GD package required for circos

brew install libgd            ## Needed to install perl GD package required for circos

brew install xz               ## Needed for bedtools compile to provide lzma.h

# Open a new terminal window

# Type the following

java -version

# I got the following output

java version "1.6.0_65"

Java(TM) SE Runtime Environment (build 1.6.0_65-b14-468)

Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-468, mixed mode)

# However, this does not work with the current IGV, install the recommended version 11

java -version

#Output should now indicate the updated or installed version of JAVA

java version "11.0.3" 2019-04-16 LTS

Java(TM) SE Runtime Environment 18.9 (build 11.0.3+12-LTS)

Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.3+12-LTS, mixed mode)

java -version

#Still shows JAVA11 as the default

java version "11.0.3" 2019-04-16 LTS

Java(TM) SE Runtime Environment 18.9 (build 11.0.3+12-LTS)

Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.3+12-LTS, mixed mode)

# To see what versions of JAVA are available on your system

/usr/libexec/java_home -verbose

Matching Java Virtual Machines (4):

    11.0.3, x86_64: "Java SE 11.0.3" /Library/Java/JavaVirtualMachines/jdk-11.0.3.jdk/Contents/Home

    1.8.0_211, x86_64: "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0_211.jdk/Contents/Home

    1.6.0_65-b14-468, x86_64: "Java SE 6" /Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home

    1.6.0_65-b14-468, i386: "Java SE 6" /Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home

# If you want to use JAVA8 specifically at the command line do the following:

/usr/libexec/java_home -v 1.8.0_211 --exec java -version

java version "1.8.0_211"

Java(TM) SE Runtime Environment (build 1.8.0_211-b12)

Java HotSpot(TM) 64-Bit Server VM (build 25.211-b12, mixed mode)

# Open a new terminal window

cd local

wget http://data.broadinstitute.org/igv/projects/downloads/2.5/IGV_2.5.2.zip

## This was the version at time of writing

unzip IGV_2.5.2.zip

cd IGV_2.5.2

# Update the igv.sh file to set Xmx2g to the appropriate value for your system

# Xmx is the maximum amount of memory you will allow IGV to use

vim igv.sh

exec java --module-path="${prefix}/lib" -Xmx16g

# 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_2.5.2/igv.sh'

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

IGV

# Open a new terminal window and move into the local folder

cd local

# Download the current release using wget

wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2

# Decompress downloaded archive, enter folder and compile

tar xvjf htslib-1.9.tar.bz2

cd htslib-1.9/

./configure

make

# This copies the relevant binaries to your $HOME/local/bin directory

make prefix=$HOME/local install

cd ~/local

wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2

tar xvjf samtools-1.9.tar.bz2

cd samtools-1.9

./configure

make

make prefix=$HOME/local install

cd ~/local

wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2

tar xvjf bcftools-1.9.tar.bz2

cd bcftools-1.9

make

make prefix=$HOME/local install

cd ~/local/

wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz

tar xvzf bedtools-2.28.0.tar.gz

cd bedtools2

make

cd bin

cp bedtools ~/local/bin

cd ~/local/

wget https://github.com/lh3/seqtk/archive/v1.3.tar.gz

tar xvzf v1.3.tar.gz

cd seqtk-1.3/

make

cp seqtk ~/local/bin

cd ~/local

wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2

tar xvjf bwa-0.7.17.tar.bz2

cd bwa-0.7.17

make

cp bwa ~/local/bin

cd ~/local

mkdir picard-2.20.1   ## (VERSION SPECIFIC FOLDER)

cd picard-2.20.1

wget https://github.com/broadinstitute/picard/releases/download/2.20.1/picard.jar

# Put a copy of the jar file in the $HOME/local/bin

cp picard.jar ~/local/bin/

cd ~/local

wget https://github.com/broadinstitute/gatk/releases/download/4.1.2.0/gatk-4.1.2.0.zip

unzip gatk-4.1.2.0.zip

cd gatk-4.1.2.0

./gatk --help          ## This works

./gatk --list          ## This ERRORS, because default java is v11 not needed v8

### PROBLEM, GATK4 requires java 8, while IGV requires java 11 so running both is a bit of a mess, I don't really need a solution beyond testing, but want java 11 as the default so IGV works without any effort. 

### SEE THE UPDATING JAVA SECTION ABOVE FOR MORE DETAILS ABOUT JAVA INSTALLS

# To call the GATK .jar file directly this works as a command after installing JAVA8 as noted above.

/usr/libexec/java_home -v 1.8.0_211 --exec java -jar $HOME/local/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar --help   

To enable as a more simple executable I created an alias as follows:

vim ~/.profile

#Add this line to the Program Alias section

alias GATK4='/usr/libexec/java_home -v 1.8.0_211 --exec java -jar $HOME/local/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar'

#Restart the terminal and test the implementation

GATK4 --help

# Original function on lines 207 and 208

def formatLocalJarCommand(localJar):

  return ["java"] + PACKAGED_LOCAL_JAR_OPTIONS + [ "-jar", localJar]

# Original error message when executing ./gatk --list

Using GATK jar /Users/jkeats/local/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar

Running:

    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Users/jkeats/local/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar --help

Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class org/broadinstitute/barclay/argparser/CommandLineProgramGroup. Method lambda$static$0(Lorg/broadinstitute/barclay/argparser/CommandLineProgramGroup;Lorg/broadinstitute/barclay/argparser/CommandLineProgramGroup;)I at index 43 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef

at org.broadinstitute.barclay.argparser.CommandLineProgramGroup.<clinit>(CommandLineProgramGroup.java:19)

at org.broadinstitute.hellbender.Main.printUsage(Main.java:384)

at org.broadinstitute.hellbender.Main.extractCommandLineProgram(Main.java:342)

at org.broadinstitute.hellbender.Main.setupConfigAndExtractProgram(Main.java:182)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:204)

at org.broadinstitute.hellbender.Main.main(Main.java:291)

# Edited function

def formatLocalJarCommand(localJar):

  return ["/usr/libexec/java_home -v 1.8.0_211 --exec java"] + PACKAGED_LOCAL_JAR_OPTIONS + [ "-jar", localJar]

# New error message when executing ./gatk --list

Using GATK jar /Users/jkeats/local/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar

Running:

    /usr/libexec/java_home -v 1.8.0_211 --exec java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Users/jkeats/local/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar --help

Traceback (most recent call last):

  File "./gatk", line 479, in <module>

    main(sys.argv[1:])

  File "./gatk", line 152, in main

    runGATK(sparkRunner, sparkSubmitCommand, dryRun, gatkArgs, sparkArgs, javaOptions)

  File "./gatk", line 328, in runGATK

    runCommand(cmd, dryrun)

  File "./gatk", line 384, in runCommand

    check_call(cmd, env=gatk_env)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 535, in check_call

    retcode = call(*popenargs, **kwargs)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 522, in call

    return Popen(*popenargs, **kwargs).wait()

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 710, in __init__

    errread, errwrite)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1335, in _execute_child

    raise child_exception

cd ~/local/

wget http://circos.ca/distribution/circos-0.69-6.tgz

tar xvzf circos-0.69-6.tgz

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

cd circos-0.69-6/bin/

# Test which required modules are available or missing

./circos -module

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

ok       1.29 Carp

ok       0.36 Clone

missing            Config::General

ok       3.40 Cwd

ok      2.145 Data::Dumper

ok       2.52 Digest::MD5

ok       2.84 File::Basename

ok       3.40 File::Spec::Functions

ok       0.23 File::Temp

ok       1.51 FindBin

missing            Font::TTF::Font

missing            GD

missing            GD::Polyline

ok       2.39 Getopt::Long

ok       1.16 IO::File

ok       0.33 List::MoreUtils

ok       1.38 List::Util

missing            Math::Bezier

ok      1.998 Math::BigFloat

ok       0.06 Math::Round

missing            Math::VecStat

ok       1.03 Memoize

ok       1.32 POSIX

ok       1.08 Params::Validate

ok       1.61 Pod::Usage

missing            Readonly

ok 2013031301 Regexp::Common

missing            SVG

missing            Set::IntSpan

missing            Statistics::Basic

ok       2.41 Storable

ok       1.17 Sys::Hostname

ok       2.02 Text::Balanced

missing            Text::Format

ok     1.9725 Time::HiRes

## Now install all the missing modules using the CPAN downloader in the terminal

sudo perl -MCPAN -e shell

## This caused some new issues, maybe TGen permissions, and I had to answer three questions:

1) Would you like to configure as much as possible automatically? [yes] yes

Warning: You do not have write permission for Perl library directories.

To install modules, you need to configure a local Perl library directory or

escalate your privileges.  CPAN can help you by bootstrapping the local::lib

module or by configuring itself to use 'sudo' (if available).  You may also

resolve this problem manually if you need to customize your setup.

2) What approach do you want?  (Choose 'local::lib', 'sudo' or 'manual') [local::lib] local::lib

3) Would you like me to automatically choose some CPAN mirror sites for you? (This means connecting to the Internet) [yes] yes

# Order use to matter, at least GD need to be done first

install GD

install Config::General

install Font::TTF::Font

install GD::Polyline

install Math::Bezier

install Math::VecStat

install Readonly

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'

cd ~/local/

wget http://circos.ca/distribution/circos-tools-0.23.tgz

tar xvzf circos-tools-0.23.tgz

cd ~/local/

# There is no version 0.69 tutorials so using the last one provided at this time

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-0.69-6/bin/circos -conf circos.conf

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

vim ~/.profile

alias CIRCOS='$HOME/local/circos-0.69-6/bin/circos'

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

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

CIRCOS -conf circos.conf

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

cd ~/local/

wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip

unzip fastqc_v0.11.8.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