Package conflicts installing AGAT

Question

[giammafer]

Hi, I am not an expert in Windows and Linux OS.

I would like to try to install AGAT on my computer. The OS is a Windows7 (64 bit installation) and I have ANACONDA Navigator 1.10.0

I have referred to the installation guide for AGAT. (https://github.com/NBISweden/AGAT#install-prerequisites)

To install the software I have opened the ANACONDA Navigator dashboard and I have selected the POWERSHELL PROMPT from which I have launched the commands.

I have chosen to install the program using BIOCONDA and this is the command:

(base) PS C:\Users\mycomputer> conda install -c bioconda agat

The output is this:

Collecting package metadata (current_repodata.json): done

Solving environment: failed with initial frozen solve.

Retrying with flexible solve.

Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

Collecting package metadata (repodata.json): done

Solving environment: failed with initial frozen solve.

Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes.

Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package vs2015_runtime conflicts for:
python=3.8 ->vc[version='>=14.1,<15.0a0'] ->vs2015_runtime[version='>=14.15.26706|>=14.27.29016|>=14.28.29325|>=14.29.30037|>=14.16.27033'] agat -> libdb -> vs2015_runtime[version='>=14.16.27012']
python=3.8 ->vs2015_runtime[version='>=14.16.27012|>=14.16.27012,<15.0a0']

Package vc conflicts for:
python=3.8 ->openssl[version='>=1.1.1f,<1.1.2a'] ->vc[version='14.|9.|>=14,<15.0a0']
python=3.8 ->vc[version='>=14.1,<15.0a0'

I have to say that I tried also other methods like the "Old school - Manually" section suggested in AGAT installation guide. From the result, it seems that some Perl modules are not found and I cannot fetch them from the channels. However, I would like to pose a question about Bioconda first and understand where I am wrong or what I did not consider checking the prerequisites for AGAT.

Thanks for your help.

[Juke34]

You might consider to use Docker or Singularity to avoid those problems.
I don't know if it is possible to with POWERSHELL PROMPT but you can try to clone the repo and run:

 conda env create -f conda_environment_AGAT.yml

[giammafer]

Yes Juke I have tried this method but does not work. If I create the environment through the .yml it seems that works. Indeed, the command:

(agat) PS C:\PoGo4Virus\AGAT-master> conda env list

shows:

# conda environments:
#
                           C:\ProgramData\Anaconda3
base                     C:\Users\mycomputer\anaconda3
agat                  *  C:\Users\mycomputer\anaconda3\envs\agat

I have downloaded manually the AGAT folder instead of to clone the folder. When I go into this folder and try to check for the dependencies this is the result:

(agat) PS C:\PoGo4Virus\AGAT-master> perl Makefile.PL

+ perl <<<<  Makefile.PL
+ CategoryInfo          : ObjectNotFound: (perl:String) [], CommandNotFoundException       
+ FullyQualifiedErrorId : CommandNotFoundException

I think that the main problem is that I am trying to install AGAT on a Windows platform. I do not have a Linux partition on this laptop but I think that I need to switch to Linux if I want to avoid such kinds of issues.

[Juke34]

Yes for bioinformatics you better to use Unix platforms. But I thought agat installation would work smoothly for AGAT. I'm not a windows person, so I cannot really help...