Install bwa, samtools & bcftools on Windows WSL (Ubuntu)

bwa, samtools, bcftools on WSL.txt

# tested on WSL 2, Ubuntu 18.04 LTS

# needed for bwa & samtools
sudo apt-get install build-essential make libz-dev -y   

# needed for samtools
sudo apt-get install cwltool libc-ares2 libhttp-parser2.7.1 libjs-bootstrap nodejs nodejs-doc python python-asn1crypto python-avro python-cachecontrol python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-html5lib python-idna python-ipaddress python-isodate python-lockfile python-mistune python-openssl python-pkg-resources python-pyparsing python-rdflib python-rdflib-jsonld python-requests python-ruamel.yaml python-schema-salad python-shellescape python-six python-sparqlwrapper python-typing python-urllib3 python-webencodings -y
sudo apt-get install libncurses5-dev -y
# sudo apt-get remove zlib1g-dev -y
sudo apt-get install zlib1g-dev -y
sudo apt-get install libbz2-dev -y
 
# bwa install:
https://github.com/lh3/bwa#getting-started

# samtools install (including htslib):
wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 -O samtools.tar.bz2
tar -xjvf samtools.tar.bz2
cd samtools-1.10
./configure
make
sudo make install
cd ..

# bcftools install (including htslib):
wget https://github.com/samtools/bcftools/releases/download/1.10.2/bcftools-1.10.2.tar.bz2 -O bcftools.tar.bz2
tar -xjvf bcftools.tar.bz2
cd bcftools-1.10.2/
./configure
make
sudo make install
cd ..