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Re: Reproducible Research Hackathon: Friday, July 3rd

From: Pjotr Prins
Subject: Re: Reproducible Research Hackathon: Friday, July 3rd
Date: Tue, 30 Jun 2020 23:57:40 -0500
User-agent: NeoMutt/20170113 (1.7.2)

We at UTHSC are game. We are struggling with an old version of the
GeneNetwork web service 1.x which is now running on a 10 year old
CentOS.  The backup time machine server died recently.

GenNetwork1 depends on Python 2.4(!) with modules that have not been
updated this century, and an older version of Apache with mod_python,
amongst other things. We would like to use the guix time-machine
feature to run older versions on demand in containers, also for the
recent GeneNetwork2 version which runs on a modern Guix stack. When we
get it to work I would like to push the older packages in Guix-Past.

Bit much for one day, but let's see where it ends.

There is no point in updating the older GeneNetwork1 instances, I mean
the code. The point really is that it is a reproducible version tied
to older scientific publications that people still can explore. 

Note that GeneNetwork requires a largisch MySQL/MariaDB (170GB)
which is also a snapshot in time. We have 5+ snapshots of that
database that go with 5+ versions of the code. We want to run them all
under Guix so we no longer have to care about the underlying Linux

With the newer GeneNetwork2 stack we are thinking of making use of
Guix timemachine to run snapshots, firing containers up on demand.
These will have to be tied with a certain version of the database, so
we have to force time points maintained outside the package Guix git
repo. The databases can be ready to run - listening on a different
port for each version. Nice challenge and it will make a great story
when it works.


On Tue, Jun 30, 2020 at 02:40:12PM +0200, simon tournier wrote:
> Hello,
> We are pleased to announce a Hackathon about Reproducible Science.
> We propose to collectively tackle some issues on *Friday, July 3rd*:
>  - identify stumbling blocks in using Guix to write end-to-end
> pipelines,
>  - document how to achieve this,
>  - feed the Guix-Past channel by other old packages,
>  - provide guix.scm for some of the ReScience C submissions.
> Feel free to contact us at if you would like to hack
> with us.
> We will meet at *9:30 CEST* on the #guix-hpc channel of
>  You can use this web client to reach us:
> (tweaking the channel name).
> Read more details at:
> Hope to see you on Friday.

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