Required binariesΒΆ

Note

This step is not needed when using the Docker version.

The binaries of bwa, samtools and GATK need to be available and executable on all nodes in the same directory which will be given as an argument to the Halvade script. In this tutorial we will use the /halvade/bin/ directory for this.

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halvadebin=/halvade/bin
cd $halvadebin

# get bwa
BWA_V=0.7.16a
wget https://github.com/lh3/bwa/releases/download/v0.7.16/bwa-${BWA_V}.tar.bz2
tar -vxjf bwa-${BWA_V}.tar.bz2
cd bwa-${BWA_V}
make
cp bwa ../
cd ../
rm -r bwa-${BWA_V} bwa-${BWA_V}.tar.bz2

# this needs to be installed on your system for samtools to be able to build:
sudo yum install -y make gcc zlib-devel bzip2-devel # fedora/centos/amazon aws/google compute etc
sudo apt-get install -y make gcc zlib1g-dev libbz2-dev # ubuntu/debian etc

# get samtools
SAMTOOLS_V=1.11 # needs to be 1.11 or later, for strelka
wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_V}/samtools-${SAMTOOLS_V}.tar.bz2
tar -vxjf samtools-${SAMTOOLS_V}.tar.bz2
cd samtools-${SAMTOOLS_V}
./configure --without-curses --disable-lzma # disable curses and lzma for amazon aws/google cloud
make
cp samtools ../
cd ../
rm -r samtools-${SAMTOOLS_V} samtools-${SAMTOOLS_V}.tar.bz2

# get GATK
GATK_V=4.1.2.0
wget https://github.com/broadinstitute/gatk/releases/download/${GATK_V}/gatk-${GATK_V}.zip
unzip -j gatk-${GATK_V}.zip gatk-${GATK_V}/gatk-package-${GATK_V}-local.jar
rm gatk-${GATK_V}.zip

# optionally Strelka2
STRELKA_V=2.9.10
wget https://github.com/Illumina/strelka/releases/download/v${STRELKA_V}/strelka-${STRELKA_V}.centos6_x86_64.tar.bz2
tar -xvf strelka-${STRELKA_V}.centos6_x86_64.tar.bz2
rm strelka-${STRELKA_V}.centos6_x86_64.tar.bz2

Now you should have these three binaries in your halvade binary folder:

  • bwa
  • samtools
  • gatk-package-${GATK_V}-local.jar

And optionally this folder:

  • strelka-${STRELKA_V}.centos6_x86_64