Question: How to install samtools v.1.2 on Ubuntu 14.0 32 bit?
1
gravatar for bioExplorer
3.1 years ago by
bioExplorer3.7k
bioExplorer3.7k wrote:

Hi,

Can anybody please tell me how to install samtools v.1.2  on Ubuntu 14.0 32 bit?

I am very new to Linux environment and NGS tools.  I have tried the following but the version is not what I want.

 

sudo apt-get install samtools

 

Please help me with the appropriate link to download samtools and the commands to install it.

 

Many thanks

samtools installation • 7.7k views
ADD COMMENTlink modified 3.1 years ago by Pierre Lindenbaum118k • written 3.1 years ago by bioExplorer3.7k

If you are new to the field and you find it a hassle to install everything you need for your work you can use http://environmentalomics.org/bio-linux/ which is a version of ubuntu with a lot of bioinformatics packages added to. However it's always better to learn how to install packages yourself. 

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Parham1.4k

Hi Parham,

thanks for the answer, however, for now I need to stick with this version.

Can you help with my initial question?

Thanks

ADD REPLYlink written 3.1 years ago by bioExplorer3.7k

This should help you install the package: http://www.htslib.org/download/

You need to download the package first and follow the above guideline. 

ADD REPLYlink written 3.1 years ago by Parham1.4k

Coming back to my question after ~3 years with this answer

1. Install conda

Go to this link and download the appropriate miniconda installler. The file should look something like this Miniconda2-latest-Linux-xxx_xx.sh

2. Follow installation steps

Follow the steps mentioned at this link to install conda

3. Activate conda

conda activate

4. Install samtools using conda

conda install -c bioconda samtools

ADD REPLYlink modified 6 days ago • written 6 days ago by bioExplorer3.7k
5
gravatar for Pierre Lindenbaum
3.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:
wget  "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2"  && tar xfj samtools-1.2.tar.bz2  && (cd samtools-1.2 && make)

 

then put samtools in your path: https://linuxconfig.org/permanently-add-a-directory-to-shell-path

export PATH=/full/path/to/samtools-1.2:${PATH}

 

 

ADD COMMENTlink written 3.1 years ago by Pierre Lindenbaum118k
1

or even shorter

wget https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2 -O - | tar xj ; ( cd samtools-1.2 ; make )
ADD REPLYlink written 3.1 years ago by piet1.6k
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