| Message ID | 20220321191918.18123-1-madalinionel.patrascu@mdc-berlin.de |
|---|---|
| State | Accepted |
| Headers | show |
| Series | [bug#54511] gnu: Add r-cytobackbone. | expand |
| Context | Check | Description |
|---|---|---|
| cbaines/comparison | success | View comparision |
| cbaines/git branch | success | View Git branch |
| cbaines/applying patch | success | View Laminar job |
| cbaines/issue | success | View issue |
Mădălin Ionel Patrașcu schreef op ma 21-03-2022 om 20:19 [+0100]:
> + (properties `((upstream-name #{.}# "CytoBackBone")))
This needs to be (upstream-name . "CytoBackBone") -- #{.}# is the
symbol containing a dot, so (upstream-name #{.}# "CytoBackBone") is a
three-element list and not a pair.
Greetings,
Maxime.
Mădălin Ionel Patrașcu schreef op ma 21-03-2022 om 20:19 [+0100]:
> + (license license:gpl2))))
Could you ask upstream if they meant gpl2 or gpl2-or-later?
Mădălin Ionel Patrașcu schreef op ma 21-03-2022 om 20:19 [+0100]: > + (description > + "Single-cell technologies are the most suitable [...] This doesn't seem a good description to me as it is one big word salad. Also see ‘(guix)Synopses and Descriptions’ for some tips. Greetings, Maxime.
Dear Maxime, This is an artifact after I run guix style. I missed it this time. Thanks for spotting this! All the best! Mădălin Ionel Patrașcu System Administrator The Berlin Institute for Medical Systems Biology (BIMSB) Max Delbrück Center (MDC) Robert-Rössle-Straße 10 House 87, room 1.10 13125 Berlin, Germany ________________________________ From: Maxime Devos <maximedevos@telenet.be> Sent: Monday, March 21, 2022 21:17 To: Patrascu, Madalin Ionel; 54511@debbugs.gnu.org Subject: [ext] Re: [bug#54511] [PATCH] gnu: Add r-cytobackbone. Mădălin Ionel Patrașcu schreef op ma 21-03-2022 om 20:19 [+0100]: > + (properties `((upstream-name #{.}# "CytoBackBone"))) This needs to be (upstream-name . "CytoBackBone") -- #{.}# is the symbol containing a dot, so (upstream-name #{.}# "CytoBackBone") is a three-element list and not a pair. Greetings, Maxime.
Dear Maxime, Thanks for the suggestion! Now, I have asked this. https://github.com/tchitchek-lab/CytoBackBone/issues/2 [https://opengraph.githubassets.com/0db2fcd2573d74d186964b02586c50768de2bd17394f06020ea67ddcba92e496/tchitchek-lab/CytoBackBone/issues/2]<https://github.com/tchitchek-lab/CytoBackBone/issues/2> License · Issue #2 · tchitchek-lab/CytoBackBone · GitHub<https://github.com/tchitchek-lab/CytoBackBone/issues/2> github.com Dear Authors, Quick question: This project is licensed under GPL-2.0-only or the license GPL-2.0-or-later can be applied? I ask this because we try to add this to Guix. https://debbugs.gnu.org/cgi/bugreport.cgi?bug=54511 Thanks and all t... All the best! Mădălin Ionel Patrașcu System Administrator The Berlin Institute for Medical Systems Biology (BIMSB) Max Delbrück Center (MDC) Robert-Rössle-Straße 10 House 87, room 1.10 13125 Berlin, Germany ________________________________ From: Maxime Devos <maximedevos@telenet.be> Sent: Monday, March 21, 2022 21:17 To: Patrascu, Madalin Ionel; 54511@debbugs.gnu.org Subject: [ext] Re: [bug#54511] [PATCH] gnu: Add r-cytobackbone. Mădălin Ionel Patrașcu schreef op ma 21-03-2022 om 20:19 [+0100]: > + (license license:gpl2)))) Could you ask upstream if they meant gpl2 or gpl2-or-later?
Dear Maxime, Bioinformatics is not my area of expertise ,and beside this, it was the end of a busy day and I wanted to finish this faster. Sorry that I didn't treat this with more attention! I will try to send again a path with a more readable description. All the best! Mădălin Ionel Patrașcu System Administrator The Berlin Institute for Medical Systems Biology (BIMSB) Max Delbrück Center (MDC) Robert-Rössle-Straße 10 House 87, room 1.10 13125 Berlin, Germany ________________________________ From: Maxime Devos <maximedevos@telenet.be> Sent: Monday, March 21, 2022 21:19 To: Patrascu, Madalin Ionel; 54511@debbugs.gnu.org Subject: [ext] Re: [bug#54511] [PATCH] gnu: Add r-cytobackbone. Mădălin Ionel Patrașcu schreef op ma 21-03-2022 om 20:19 [+0100]: > + (description > + "Single-cell technologies are the most suitable [...] This doesn't seem a good description to me as it is one big word salad. Also see ‘(guix)Synopses and Descriptions’ for some tips. Greetings, Maxime.
I moved this to bioinformatics.scm. Thanks!
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 55d397e5cf..6f5a040f65 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10066,6 +10066,44 @@ (define-public r-consensusclusterplus cluster count and membership by stability evidence in unsupervised analysis.") (license license:gpl2))) +;; It doesn't have a system of releases. This package depends on a bioconductor +;; input. +(define-public r-cytobackbone + (let ((commit "4c1a0a35cc5ae1f8f516127cec92351d96fe26e7") (revision "1")) + (package + (name "r-cytobackbone") + (version (git-version "1.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tchitchek-lab/CytoBackBone") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ahiad14zcgdk42xzw5xryic2ibn2l8lkrcdvl2b5sz2js028yb3")))) + (properties `((upstream-name #{.}# "CytoBackBone"))) + (build-system r-build-system) + (propagated-inputs (list r-flowcore r-flowutils r-fnn r-ggplot2 + r-preprocesscore)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tchitchek-lab/CytoBackBone") + (synopsis + "Merging of phenotype information from different cytometric profiles") + (description + "Single-cell technologies are the most suitable techniques for the +characterization of cells by the differential expression of the molecules that +define their roles and functions in tissues. Among these techniques, mass +cytometry represents a leap forward by increasing the number of available +measurements to approximately 40 cell markers. Thanks to this technology, +detailed immune responses were described in several diseases. However, the +study of immune responses, such as that due to viral infections or auto-immune +diseases, could be further improved by increasing the number of simultaneously +measurable markers. To increase this number, we designed an algorithm, named +@code{CytoBackBone}, which combines phenotypic information of different +cytometric profiles obtained from different cytometry panels.") + (license license:gpl2)))) + (define-public r-cytolib (package (name "r-cytolib")