From: zimoun <zimon.toutoune@gmail.com>
To: Konrad Hinsen <konrad.hinsen@fastmail.net>, gwl-devel@gnu.org
Subject: Re: Managing data files in workflows
Date: Fri, 26 Mar 2021 08:02:40 +0100 [thread overview]
Message-ID: <86v99ebdnz.fsf@gmail.com> (raw)
In-Reply-To: <m18s6bk12w.fsf@ordinateur-de-catherine--konrad.home>
Hi Konrad,
It does not answer your concrete question but instead open a new
one. :-)
Well, I never finished this drafts, maybe it can be worth to discuss
1. how to deal with data?
2. on which does the workflow trigger a recomputation?
Cheers,
simon
-------------------- Start of forwarded message --------------------
Hi,
The recent features of the Guix Workflow Language [1] are really neat!
The end-to-end paper by Ludo [2] is also really cool! For the online
Guix Day back on December, it would have been cool to be able to
distribute the videos via a channel. Or it could be cool to have all
the material talks [3] in a channel.
But a package is not the right abstraction here. First because a “data”
can have multiple sources, second data can be really large and third
data are not always readable as source and do not have an output; data
are kind of fixed output. (Code is data but data is not code. :-))
Note that data is already fetched via packages, see
’r-bsgenome-hsapiens-ucsc-hg19’ or ’r-bsgenome-hsapiens-ucsc-hg38’
(’guix import’ reports ~677.3MiB and ’guix size’ reports ~748.0 MiB). I
am not speaking about these.
If I might, let take the example of Lars’s talk from Guix Day:
<https://www.psycharchives.org/handle/20.500.12034/3938>
There is 2 parts: the video itself and the slides. Both are part of the
same. Another example is Konrad’s paper:
<https://dx.doi.org/10.1063/1.5054887>
with the paper and the supplementary (code+data).
With these 2 examples, ’package’ with some tweaks could be used. But
for the data I deal at work, the /gnu/store is not designed for that.
To fix the idea, about (large) genomics study, let say 100 patients and
0.5-10GB data for each. In addition to genomics reference which means a
couple of GB. At work, these days we do not have too much new genomic
projects; let say there 3 projects in parallel. I let you complete the
calculus. ;-)
There is 3 levels:
1- the methods for fetching: URL (http or ftp), Git, IPFS, Dat, etc.
2- the record representing a “data”
3- how to effectively locally store and deal with it
And if it makes sense that a ’data’ is an input of a
’package’, and conversely, is a question.
Long time ago, with GWL folks we discussed “backend”, as git-annex or
something else, but from my understanding, it would answer about #3 and
what git-annex accepts as protocol would answer to #1. Remaining #2.
In my project, I would like to have 3 files: manifest describing which
tools, channels describing at which version, and data describing how to
fetch the data. Then, I have the tool to work reproducibly: I can apply
a workflow (GWL, my custom Python script, etc.).
1: <https://guixwl.org/>
2: <https://hpc.guix.info/blog/2020/06/reproducible-research-articles-from-source-code-to-pdf/>
3: <https://git.savannah.gnu.org/cgit/guix/maintenance.git/tree/talks>
Cheers,
simon
-------------------- End of forwarded message --------------------
next prev parent reply other threads:[~2021-03-26 7:06 UTC|newest]
Thread overview: 15+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-03-25 9:57 Managing data files in workflows Konrad Hinsen
2021-03-26 7:02 ` zimoun [this message]
2021-03-26 12:46 ` Konrad Hinsen
2021-03-26 8:47 ` Ricardo Wurmus
2021-03-26 12:30 ` Konrad Hinsen
2021-03-26 12:54 ` Konrad Hinsen
2021-03-26 13:13 ` Ricardo Wurmus
2021-03-26 15:36 ` Konrad Hinsen
2021-04-01 13:27 ` Ricardo Wurmus
2021-04-02 8:41 ` Konrad Hinsen
2021-04-07 11:38 ` Ricardo Wurmus
2021-04-08 7:28 ` Konrad Hinsen
2021-05-03 9:18 ` Ricardo Wurmus
2021-05-03 11:58 ` zimoun
2021-05-03 13:47 ` Ricardo Wurmus
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=86v99ebdnz.fsf@gmail.com \
--to=zimon.toutoune@gmail.com \
--cc=gwl-devel@gnu.org \
--cc=konrad.hinsen@fastmail.net \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.