Bioinformatics for Cancer Genomics 2019 - Post Workshop

Post Workshop Access and Instructions

References

You can download references and indexes for commonly analyzed organisms from Igenomes

Data Sets

The data sets in the workshop can be downloaded from below. If your download speed is slow, please contact zhibin<at>gmail.com who can provide you with the alternative methods.

AWS Image

The AWS AMI for 2019 CBW workshop is publicly avaiable at US East region. AMI name: CBW_2019, AMI ID: ami-0b3a39967ade13fbb. Please let us know if you need it in other regions.

Tools and Installation Instructions

bioperl

sudo apt install expat
perl -MCPAN -e shell
install Module::Build
o conf prefer_installer MB
o conf commit
d /bioperl/
install CJFIELDS/BioPerl-1.007002.tar.gz

R

add “deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/” into /etc/apt/sources.list.d/R.list

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo apt update
sudo apt-get install r-base r-base-dev

abyss

sudo apt-get install abyss

bam-readcount

git clone https://github.com/genome/bam-readcount.git
cmake bam-readcount/
make

bamtools

git clone git://github.com/pezmaster31/bamtools.git
cd bamtools
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/usr/local ..
make
sudo make install

bedops

wget https://github.com/bedops/bedops/releases/download/v2.4.35/bedops_linux_x86_64-v2.4.35.tar.bz2
tar -jxf bedops_linux_x86_64-v2.4.35.tar.bz2

bedtools

wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz
tar zxf bedtools-2.27.1.tar.gz
cd bedtools2/
make
sudo make install

blast+

wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.8.1+-x64-linux.tar.gz
tar zxf ncbi-blast-2.8.1+-x64-linux.tar.gz

bowtie2

wget http://cfhcable.dl.sourceforge.net/project/bowtie-bio/bowtie2/2.3.4.3/bowtie2-2.3.4.3-linux-x86_64.zip
unzip bowtie2-2.3.4.3-linux-x86_64.zip

bwa

wget https://newcontinuum.dl.sourceforge.net/project/bio-bwa/bwa-0.7.17.tar.bz2
tar -jxvf bwa-0.7.17.tar.bz2
cd bwa-0.7.17/
make

canu

wget wget https://github.com/marbl/canu/releases/download/v1.8/canu-1.8.Linux-amd64.tar.xz
xz -dv canu-1.8.Linux-amd64.tar.xz
tar -xvf canu-1.8.Linux-amd64.tar

Centrifuge

wget https://github.com/infphilo/centrifuge/archive/v1.0.4-beta.tar.gz
tar zxf v1.0.4-beta.tar.gz
cd centrifuge-1.0.4-beta/
make

DELLY

wget https://github.com/dellytools/delly/releases/download/v0.8.1/delly_v0.8.1_linux_x86_64bit
mv delly_v0.8.1_linux_x86_64bit delly
chmod +x delly

FastQC

wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip
unzip fastqc_v0.11.8.zip
cd FastQC
chmod +x fastqc

Note: if you get error: Exception in thread “Thread-1” java.awt.AWTError: Assistive Technology not found: org.GNOME.Accessibility.AtkWrapper You can comment out the following line in /etc/java-8-openjdk/accessibility.properties

assistive_technologies=org.GNOME.Accessibility.AtkWrapper

or run the following before you run fastqc

export _JAVA_OPTIONS=-Djavax.accessibility.assistive_technologies=

Flexbar

sudo apt install flexbar

GATK

download from https://www.broadinstitute.org/gatk/download (need to log in)
unzip gatk-4.1.0.0.zip

gffcompare

wget http://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.10.6.Linux_x86_64.tar.gz
tar zxf gffcompare-0.10.6.Linux_x86_64.tar.gz

GMAP

wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2018-07-04.tar.gz
tar -zxf gmap-gsnap-2018-07-04.tar.gz
cd gmap-2018-07-04
./configure
make
sudo make install

HISAT2

wget http://ccb.jhu.edu/software/hisat2/dl/hisat2-2.1.0-Linux_x86_64.zip
unzip hisat2-2.1.0-Linux_x86_64.zip && rm hisat2-2.1.0-Linux_x86_64.zip

HMMER

wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
tar zxf hmmer-3.1b2-linux-intel-x86_64.tar.gz

HTSeq

sudo pip install HTSeq

JellyFish

wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.10/jellyfish-linux
chmod +x jellyfish-linux

kallisto

wget https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_linux-v0.45.0.tar.gz
tar zxf kallisto_linux-v0.45.0.tar.gz

medaka

need to modify medaka_variant and medaka_consensus to use python3 because the system default python is version 2.

sudo pip3 install medaka

minimap2

curl -L https://github.com/lh3/minimap2/releases/download/v2.16/minimap2-2.16_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.16_x64-linux/minimap2

MultiQC

pip install multiqc

MuTect

You need to sign in to download from https://software.broadinstitute.org/cancer/cga/mutect_download

unzip muTect-1.1.4-bin.zip

Picard

wget https://github.com/broadinstitute/picard/releases/download/2.18.26/picard.jar

pilon

wget https://github.com/broadinstitute/pilon/releases/download/v1.23/pilon-1.23.jar

QUAST

wget wget https://downloads.sourceforge.net/project/quast/quast-5.0.2.tar.gz
python ./setup.py build
sudo python ./setup.py install

racon

wget https://github.com/isovic/racon/releases/download/1.3.2/racon-v1.3.2.tar.gz
tar zxf racon-v1.3.2.tar.gz
cd racon-v1.3.2/
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make

regtools

wget https://github.com/griffithlab/regtools/archive/0.5.0.tar.gz
cd regtools-0.5.0
mkdir build
cd build/
cmake ..
make

RSEM

wget https://github.com/deweylab/RSEM/archive/v1.3.1.tar.gz
tar zxf v1.3.1.tar.gz
cd RSEM-1.3.1/
make
sudo make ebseq (need ‘blockmodeling’, ‘testthat’ R packages)
sudo make install

RSeQC

sudo pip install RSeQC

Salmon

wget https://github.com/COMBINE-lab/salmon/releases/download/v0.12.0/salmon-0.12.0_linux_x86_64.tar.gz
tar xzf salmon-0.12.0_linux_x86_64.tar.gz

SAMStat

needs samtools to be installed first.

wget http://downloads.sourceforge.net/project/samstat/samstat-1.5.1.tar.gz
tar -xzvf samstat-1.5.1.tar.gz
cd samstat-1.5.1/
./configure
make
sudo make install

samtools

wget https://downloads.sourceforge.net/project/samtools/samtools/1.9/samtools-1.9.tar.bz2
tar -jxvf samtools-1.9.tar.bz2
cd samtools-1.9
make
sudo make install

snpEff

wget https://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip
unzip snpEff_latest_core.zip

SPAdas

wget http://cab.spbu.ru/files/release3.13.0/SPAdes-3.13.0-Linux.tar.gz
tar xvf SPAdes-3.13.0-Linux.tar.gz

STAR

wget https://github.com/alexdobin/STAR/archive/2.7.0c.tar.gz
tar -xzf 2.7.0c.tar.gz

STAR-Fusion

wget https://github.com/STAR-Fusion/STAR-Fusion/releases/download/STAR-Fusion-v1.5.0/STAR-Fusion-v1.5.0.FULL.tar.gz
tar zxf STAR-Fusion-v1.5.0.FULL.tar.gz

Strelka

wget https://github.com/Illumina/strelka/releases/download/v2.9.10/strelka-2.9.10.release_src.tar.bz2
tar -jxf strelka-2.9.10.release_src.tar.bz2
cd strelka-2.9.10.release_src
mkdir build && cd build
../configure
make -C .
sudo make install
put /usr/local/libexec into PATH

stringtie

wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.5.Linux_x86_64.tar.gz
tar zxf stringtie-1.3.5.Linux_x86_64.tar.gz

tophat

wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz
tar -zxf tophat-2.1.1.Linux_x86_64.tar.gz

TransDecoder

wget https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v5.5.0.tar.gz
tar zxf TransDecoder-v5.5.0.tar.gz

Trimmomatic

wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
unzip Trimmomatic-0.38.zip

Trinity

wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.8.4.tar.gz
tar -zxvf Trinity-v2.8.4.tar.gz
cd trinityrnaseq-Trinity-v2.8.4
make
make plugins

Trinotate

wget https://github.com/Trinotate/Trinotate/archive/Trinotate-v3.1.1.tar.gz
tar zxf Trinotate-v3.1.1.tar.gz