From: zimoun <zimon.toutoune@gmail.com>
To: Ricardo Wurmus <rekado@elephly.net>
Cc: 54787@debbugs.gnu.org
Subject: bug#54787: importer Bioconductor: no tarball, only Git
Date: Tue, 12 Apr 2022 18:25:51 +0200 [thread overview]
Message-ID: <87ilre5kvk.fsf@gmail.com> (raw)
In-Reply-To: <874k2zzj9p.fsf@elephly.net> (Ricardo Wurmus's message of "Mon, 11 Apr 2022 18:15:39 +0200")
Hi Ricardo,
On lun., 11 avril 2022 at 18:15, Ricardo Wurmus <rekado@elephly.net> wrote:
> zimoun <zimon.toutoune@gmail.com> writes:
>
>> $ guix import cran -a bioconductor CHETAH
>> guix import: warning: failed to retrieve package information from
>> https://cran.r-project.org/web/packages/CHETAH/DESCRIPTION: 404 (Not Found)
>> guix import: error: failed to download description for package 'CHETAH'
>>
>> The reason is because there is no source package. Only the Git source
>> repo.
>
> We should finally switch to fetching the sources from Git. I wonder why
> we haven’t done this earlier.
Because, maybe, we have just finished the janitor work cleaning the
files cran.scm, bioconductor.scm and bioinformatics.scm. :-)
> I guess we should do this gradually to avoid mass updates, so perhaps we
> should introduce bioconductor-git-reference and switch over packages one
> by one.
First, note that annotations do not have Git repo; at least not always,
e.g.,
<https://bioconductor.org/packages/release/data/annotation/html/GenomeInfoDbData.html>
Second, if we go for something like:
--8<---------------cut here---------------start------------->8---
(define* (bioconductor-git-reference name #:optional
(release %bioconductor-version))
"Return a <git-reference> for the R package archive on Bioconductor for the
RELEASE corresponding to NAME."
(git-reference
(url (string-append %bioconductor-git-url name))
(commit (string-append "RELEASE_" (string-replace-substring
%bioconductor-version "." "_")))))
--8<---------------cut here---------------end--------------->8---
then, it raises the question: import/cran.scm or build-system/r.scm ?
i.e., do we put a module dependency against (guix git-download) for the
r-build-system or not?
TeXLive already has a dependency to svn-download, so why not.
Well, I am also in favor to break the API and move %bioconductor-version
and %bioconductor-url to (guix build-system r). WDYT? It would
simplify some things (#36805 and #39885), I guess.
Third, the adjustments of the importer require a large cup of coffee.
Back to CHETAH, note that
guix import cran -a git htpps://git.bioconductor.org/CHETAH
works but it points to master instead of RELEASE_3_14. Well, I am not
very familiar with the Bioconductor workflow for their release.
Last, using this in gnu/packages/bioconductor.scm,
--8<---------------cut here---------------start------------->8---
(define-public r-chetah
(package
(name "r-chetah")
(version "1.11.2")
(source
(origin
(method git-fetch)
(uri (bioconductor-git-reference "CHETAH"))
(file-name (git-file-name name version))
(sha256
(base32 "021v5831zqdy4pirfsb35kbnz8kmz4lxqc4cwi55qgd6r081xlgh"))))
(properties `((upstream-name . "CHETAH")))
(build-system r-build-system)
(propagated-inputs
(list r-biodist
r-corrplot
r-cowplot
r-dendextend
r-ggplot2
r-gplots
r-pheatmap
r-plotly
r-reshape2
r-s4vectors
r-shiny
r-singlecellexperiment
r-summarizedexperiment))
(native-inputs (list r-knitr))
(home-page "https://git.bioconductor.org/packages/CHETAH")
(synopsis "Fast and accurate scRNA-seq cell type identification")
(description
"CHETAH (CHaracterization of cEll Types Aided by Hierarchical classification) is
an accurate, selective and fast scRNA-seq classifier. Classification is guided
by a reference dataset, preferentially also a scRNA-seq dataset. By
hierarchical clustering of the reference data, CHETAH creates a classification
tree that enables a step-wise, top-to-bottom classification. Using a novel
stopping rule, CHETAH classifies the input cells to the cell types of the
references and to \"intermediate types\": more general classifications that ended
in an intermediate node of the tree.")
(license #f)))
--8<---------------cut here---------------end--------------->8---
it just builds with,
./pre-inst-env guix build r-chetah
WDYT?
Cheers,
simon
next prev parent reply other threads:[~2022-04-12 16:27 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-04-08 11:48 bug#54787: importer Bioconductor: no tarball, only Git zimoun
2022-04-11 16:15 ` Ricardo Wurmus
2022-04-12 16:25 ` zimoun [this message]
2022-04-14 11:43 ` Ricardo Wurmus
2022-04-14 12:59 ` zimoun
2022-04-14 13:57 ` Ricardo Wurmus
2022-04-14 15:03 ` zimoun
2022-04-14 14:04 ` Maxime Devos
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