Question: install some bioinformatic sofwares without root
0
gravatar for lkianmehr
3 months ago by
lkianmehr30
France
lkianmehr30 wrote:

hello to all

just to know whether is there any way to install software such as bwa and samtools on the server without the need to be user or permission of root? *

thanks in advance

install software • 242 views
ADD COMMENTlink modified 3 months ago by genomax57k • written 3 months ago by lkianmehr30
3
gravatar for jrj.healey
3 months ago by
jrj.healey7.8k
United Kingdom
jrj.healey7.8k wrote:

Yep. The easiest way (in my opinion) is through the conda package manager:

1. Install conda:

Go to https://conda.io/miniconda.html, download and run the installer (you can also use Anaconda instead of Miniconda if you want more packages preinstalled). I would allow all the defaults unless you specifically need to to go in to a particular directory.

2. Install packages

Once you have a working conda command, you can install almost everything you're likely to need with it these days (and it does it all 'locally' without admin permissions needed).

BWA:

conda install -c bioconda bwa

similarly, samtools would be:

conda install -c bioconda samtools

You can search (either on the commandline with conda search <name>) or on the website ( https://anaconda.org/bioconda ) for other packages.

This provides one advantage over just building the software locally, in that it will also do the necessary $PATH manipulations so that you can call the software without having to provide the exact filepath.

ADD COMMENTlink modified 3 months ago • written 3 months ago by jrj.healey7.8k

not lookng for grammar mistakes, but could you update "install" in "conda isntall -c. Thanks.

ADD REPLYlink written 3 months ago by cpad01129.5k

Ah yeah, well spotted.

ADD REPLYlink written 3 months ago by jrj.healey7.8k
1
gravatar for Jeffin Rockey
3 months ago by
Jeffin Rockey720
Karimannoor
Jeffin Rockey720 wrote:

You need not have to have root permission to use both the tools above.

Go to the webpage, copy the download link.

Come to your server, use wget or curl to download the file.

Extract and go inside the folder and do a build if necessary. Once built, you can use the binary files just like that.

The root permission would come necessary only if you need to INSTALL things system wide or so.

ADD COMMENTlink written 3 months ago by Jeffin Rockey720
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