Question

Installation of libraries as non-root user in server without internet connection

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4.2 years ago

RiccPicc ▴ 10

Hi everyone.

I want to use MAUVE to align 6 Drosophila genomes in order to use the alignment for a phylogeomic study. Due to the big amount of data, I cannot use my PC to perform that operation, so I use a UNIX server with no internet connection where I am not the root.

I tried to run MAUVE simply running the linux version from command line, but it raises several errors, which are often core dump. I guess it's because I should install locally this software, so i decided to follow this guide. The problem is that, since I am not the root, I have not the permission to install these required libraries. I tried to set as $HOME my folder, where I have all permissions, to change the libraries directory and the bin directory. Still I cannot install them. Can someone help me? Thank you.

MAUVE library libraries unix • 1.7k views

ADD COMMENT • link updated 4.2 years ago by antonioggsousa 3.2k • written 4.2 years ago by RiccPicc ▴ 10

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Have you tried install instructions in this guide? It does not look like you need any special libraries on unix but you will need Oracle java. If Java is not available then getting that on your server (in your user space) would take some effort.

ADD REPLY • link 4.2 years ago by GenoMax 146k

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The core dump error appears when I use them (progressiveMauve and mauveAligner). For that I want to try to install from source.

ADD REPLY • link 4.2 years ago by RiccPicc ▴ 10

score 3 · Answer 1 · 2020-08-26

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4.2 years ago

ATpoint 85k

I suggest you talk to the administrator of that cluster to get your software installed. Having no internet does not allow using package managers. Docker or singularity containers which you build on your local machine and then export could do the trick.

ADD COMMENT • link 4.2 years ago by ATpoint 85k

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Thank you ATpoint! I am trying to use singularity now and build a container with MAUVE. Let's hope it works!

Edit: unfortunately there are a lot of problems in installing all dependencies... I have also tried to build a container through conda and use it but it does not work either.

ADD REPLY • link 4.2 years ago by RiccPicc ▴ 10

score 1 · Answer 2 · 2020-08-26

Hi,

You can install conda(installation guide: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html ; download of the installation script: https://docs.conda.io/en/latest/miniconda.html ) and then Mauve through bioconda: https://anaconda.org/bioconda/mauve

Conda does not require root permissions (actually it is not convenient to install conda with root permissions as well software with conda). Though if you do not have internet connection it will be far more difficult. I think you can install locally and then move the miniconda3 folder to the server, but not 100% sure if this will work, because you might need to migrate too the configuration files etc.

I hope this helps to solve your problem,

António