Question: How to install samtools v.1.2 on Ubuntu 14.0 32 bit?
1
gravatar for lakhujanivijay
4.4 years ago by
lakhujanivijay5.1k
India
lakhujanivijay5.1k 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 • 9.0k views
ADD COMMENTlink modified 4.4 years ago by Pierre Lindenbaum129k • written 4.4 years ago by lakhujanivijay5.1k

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 5 months ago by RamRS27k • written 4.4 years ago by Parham1.5k

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 4.4 years ago by lakhujanivijay5.1k

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 modified 5 months ago by RamRS27k • written 4.4 years ago by Parham1.5k

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 5 months ago by RamRS27k • written 15 months ago by lakhujanivijay5.1k
5
gravatar for Pierre Lindenbaum
4.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k 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 modified 5 months ago by RamRS27k • written 4.4 years ago by Pierre Lindenbaum129k
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 modified 5 months ago by RamRS27k • written 4.4 years ago by piet1.7k
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