Question

install some bioinformatic sofwares without root

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5.8 years ago

lkianmehr ▴ 100

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

software install • 4.6k views

ADD COMMENT • link updated 5.8 years ago by GenoMax 141k • written 5.8 years ago by lkianmehr ▴ 100

score 5 · Accepted Answer · 2018-07-16

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.

score 1 · Accepted Answer · 2018-07-16

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.