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

I'm using a server at work and their version of samtools and bwa is way outdated.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.

centos samtools
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updated by Ram Ram • written by kristina.mahan kristina.mahan 
brew install samtools
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written by cpad0112 cpad0112

4 answers

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.

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written by GenoMax GenoMax

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
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written by 5heikki 5heikki

Epel-release might have this

This worked for me on a fresh 2019 Amazon Cloud CentOS instance

 sudo amazon-linux-extras install epel
 sudo yum install samtools

Probably on a non-amazon cloud CentOS

 sudo yum install epel-release
 sudo yum install samtools

Of course on ubuntu/debian I think samtools is in stable so you can just

 sudo apt install samtools
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written by cmdcolin cmdcolin

Note that in 2019, the centos version is samtools 0.1.19, so no CRAM support etc. Recommend linuxbrew for package manager solution on CentOS if new version is needed

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written by cmdcolin cmdcolin

OPs question (13 months back) was how to install things without sudo, still every command you gave contains it. Two good answers (compile from scratch and use a package manager such as conda) have already been given. Could you remove this answer as it does not add to the actual problem?

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written by ATpoint ATpoint

I'll remove my answer only because it is true that the title contained information about not wanting to use sudo. That said, I find your tone rude, I am just trying to contribute to the community

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written by cmdcolin cmdcolin

Even if all the features you care about were in 0.1.19 modern Samtools is significantly faster now than the old 0.1.19 release. I'm staggered to hear that Centos is still shipping such an outdated version. If they're this tardy with Samtools I wonder what other packages they're behind on. Seems like a good reason to switch distro.

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written by jkbonfield jkbonfield

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

brew install samtools

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written by cmdcolin cmdcolin

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