[bug#54511] gnu: Add r-cytobackbone.
Commit Message
* gnu/packages/bioconductor.scm (r-cytobackbone): New variable.
---
gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
Comments
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!
@@ -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")