Does anybody know how to do a local install of samtools on centos without using sudo?

Question

[kristina.mahan]

I'm using a server at work and their version of samtools and bwa is way outdated. I asked the server guy to update them and he can't do it right now and told me to install these tools locally. I'm having trouble finding a way to install these items locally without using sudo. There's a few dependencies required for samtools- any tips would be greatly appreciated.

[cpad0112]

brew install samtools

Answer 1

[GenoMax]

Take a look at conda. @finswimmer wrote a nice tutorial recently for it: Creating workflows with snakemake and conda No sudo should be needed. conda automatically installs necessary dependencies.

[kristina.mahan]

This worked great! Thanks!

Answer 2

[5heikki]

With Samtools just set /where/to/install somewhere where you can write

cd samtools-1.x    # and similarly for bcftools and htslib
./configure --prefix=/where/to/install
make
make install

With BWA you need to do even less, just clone it to somewhere where you can write

git clone https://github.com/lh3/bwa.git
cd bwa; make

Answer 3

[cmdcolin]

Download linuxbrew https://docs.brew.sh/Homebrew-on-Linux

brew install samtools