Problem when installing pigx-sars-cov2-ww

[C. Tuñí i Domínguez]

Hello!

I'm trying to install pigx-sars-cov2-ww via guix using guix install but I'm runing into the following error:

guix install: error: pigx-sars-cov2-ww: unknown package

I know this has to do with adding custom guix channels to the channels.scm file but I can't find the specific information on those channels so I can add them.

Thank you very much for your time and help!

Cristina

[Ricardo Wurmus]

Hi,

> I'm trying to install pigx-sars-cov2-ww via guix using guix
> install but I'm runing into the following error:
> guix install: error: pigx-sars-cov2-ww: unknown package

This means that your version of Guix is too old. You can confirm
this with “guix describe”.

Run “guix pull” to update to a more recent version, which includes
the package “pigx-sars-cov2-ww”.

--
Ricardo

[C. Tuñí i Domínguez]

Good afternoon Ricardo,

Thank you for your invaluable help! I did run the "guix pull" command several times but, for reasons unknown to me, it did not work until now.

Now I am able to run the pipeline.

Thank you again!

Cristina

El dia dilluns, 8 de novembre de 2021 a les 15:32:42 UTC+1, Ricardo Wurmus va escriure:

[Ricardo Wurmus]

Hi Cristina,

> I did run the "guix pull" command several times but, for reasons
> unknown to me, it did not work until now.

If the command completed without error the problem may have been
that your shell had cached an old location for the command “guix”.
You can use “type guix” to see what executable your shell will
execute when you tell it to run “guix”.

It should resolve to ~/.config/guix/current/bin/guix, because
that’s the location that a successful invocation of “guix pull”
will update.

Sometimes the shell won’t update the cached association and
starting a new shell session (e.g. by opening a new terminal or
logging out and in again) fixes the problem.

> Now I am able to run the pipeline.

Excellent!

--
Ricardo

[Charles Foster]

Hi Ricardo,

I'm also running into issues with installing pigx-sars-cov2-ww. I'm completely new to guix, and have only installed it to try out the pigx-sars-cov2-ww pipeline. Despite trying out a 'guix pull', and it finishing correctly, I still get the following error after running 'guix package -i pigx-sars-cov-2-ww': "guix package: error: pigx-sars-cov-2-ww: unknown package".

As you suggested above, I tried using "type guix". The following is output: "guix is /home/cfos/.config/guix/current/bin/guix". Output of "guix describe":

Generation 3    Dec 07 2021 15:02:44    (current)
  guix 05deb26
    repository URL: https://git.savannah.gnu.org/git/guix.git
    branch: master
    commit: 05deb26be92c314b6a60ed2ca93596b895515ca6

Do you have any suggestions? I'd really love to try out the pipeline for our wastewater surveillance, but the alternative format of installation compared to most other pipeline (e.g. using something like 'mamba env create -f environment.yml') is making it difficult.

Cheers,

Charles

[Ricardo Wurmus]

Hi Charles,

> I'm also running into issues with installing pigx-sars-cov2-ww. I'm completely new to guix, and have only
> installed it to try out the pigx-sars-cov2-ww pipeline. Despite trying out a 'guix pull', and it finishing
> correctly, I still get the following error after running 'guix package -i pigx-sars-cov-2-ww': "guix package:
> error: pigx-sars-cov-2-ww: unknown package".

The package is called “pigx-sars-cov2-ww” but you wrote
“pigx-sars-cov-2-ww”, which does not exist.

Please use “guix install pigx-sars-cov2-ww” and you should be all set.

--
Ricardo

[Charles Foster]

Hi Ricardo,

Thanks - the package is now installing. The original command I was using came straight from the github page (https://github.com/BIMSBbioinfo/pigx_sarscov2_ww), so you might want to correct the installation guide there, if possible :)

"Installation via Guix (recommended)

You can install this pipeline with all its dependencies using GNU Guix:

guix package -i pigx-sars-cov-2-ww"

Thanks,

Charles

[Ricardo Wurmus]

Charles Foster <charles...@gmail.com> writes:

> Thanks - the package is now installing. The original command I was using came straight from the github
> page (https://github.com/BIMSBbioinfo/pigx_sarscov2_ww), so you might want to correct the installation
> guide there, if possible :)

Thanks for pointing this out!
We’ll fix it. And sorry for misleading you there.

--
Ricardo