Re: branch master updated: gnu: Add r-bisquerna.
On Thu, 2020-09-10 at 13:31 +0200, Ricardo Wurmus wrote: > Roel Janssen writes: > > > > > +(define-public r-bisquerna > > > > + (package > > > > + (name "r-bisquerna") > > > > + (version "1.0.4") > > > > + (source (origin > > > > +(method url-fetch) > > > > +(uri (cran-uri "BisqueRNA" version)) > > > > +(sha256 > > > > + (base32 > > > > + "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijl > > > > m3jw > > > > 2" > > > > > > Why is this in (gnu packages bioinformatics) and not in (gnu > > > packages > > > cran)? > > > > It seemed so "bioinformatics"-specific. But you're right, it's a > > CRAN > > package, so that may be a better fit. Shall I move it to CRAN? > > If you have time to do that, yes please. Some time ago I started a > half-hearted migration of R packages from (gnu packages > bioinformatics) > to (gnu packages cran) and (gnu packages bioconductor). It’s not > supremely important, but I think in the long term we’d like to have > CRAN > things in (gnu packages cran) and Bioconductor things in (gnu > packages > bioconductor), because it’s deliciously unsurprising. :) I fully agree that it would be nice to have all packages originating from CRAN in (gnu packages cram) and all things Bioconductor in (gnu packages bioconductor). I moved r-bisquerna and lowercased its synopsis in 66be746dc0c0f4ba3d748ed8d0983b2f9afdace8. Kind regards, Roel Janssen
Re: branch master updated: gnu: Add r-bisquerna.
zimoun writes: > On Thu, 10 Sep 2020 at 13:30, Ricardo Wurmus wrote: > >> > It seemed so "bioinformatics"-specific. But you're right, it's a CRAN >> > package, so that may be a better fit. Shall I move it to CRAN? >> >> If you have time to do that, yes please. Some time ago I started a >> half-hearted migration of R packages from (gnu packages bioinformatics) >> to (gnu packages cran) and (gnu packages bioconductor). It’s not >> supremely important, but I think in the long term we’d like to have CRAN >> things in (gnu packages cran) and Bioconductor things in (gnu packages >> bioconductor), because it’s deliciously unsurprising. :) > > I agree. And it is also on my TODO but the Copyright lines lead to a > boring task. :-) It becomes a little easier with “git log --grep=package-name”. > Does it make sense to add a subsection to: > https://guix.gnu.org/manual/devel/en/guix.html#Packaging-Guidelines > about R packages? Perhaps not. I think it may not be necessary because we don’t have that many people contributing R packages to us and the manual already has a lot of information that might be overwhelming. So far we’ve been doing fine without it. It’s a really minor point, in my opinion. -- Ricardo
Re: branch master updated: gnu: Add r-bisquerna.
On Thu, 10 Sep 2020 at 13:30, Ricardo Wurmus wrote: > > It seemed so "bioinformatics"-specific. But you're right, it's a CRAN > > package, so that may be a better fit. Shall I move it to CRAN? > > If you have time to do that, yes please. Some time ago I started a > half-hearted migration of R packages from (gnu packages bioinformatics) > to (gnu packages cran) and (gnu packages bioconductor). It’s not > supremely important, but I think in the long term we’d like to have CRAN > things in (gnu packages cran) and Bioconductor things in (gnu packages > bioconductor), because it’s deliciously unsurprising. :) I agree. And it is also on my TODO but the Copyright lines lead to a boring task. :-) Does it make sense to add a subsection to: https://guix.gnu.org/manual/devel/en/guix.html#Packaging-Guidelines about R packages? Cheers, simon
Re: branch master updated: gnu: Add r-bisquerna.
Roel Janssen writes: >> > +(define-public r-bisquerna >> > + (package >> > + (name "r-bisquerna") >> > + (version "1.0.4") >> > + (source (origin >> > +(method url-fetch) >> > +(uri (cran-uri "BisqueRNA" version)) >> > +(sha256 >> > + (base32 >> > + "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw >> > 2" >> >> Why is this in (gnu packages bioinformatics) and not in (gnu packages >> cran)? > > It seemed so "bioinformatics"-specific. But you're right, it's a CRAN > package, so that may be a better fit. Shall I move it to CRAN? If you have time to do that, yes please. Some time ago I started a half-hearted migration of R packages from (gnu packages bioinformatics) to (gnu packages cran) and (gnu packages bioconductor). It’s not supremely important, but I think in the long term we’d like to have CRAN things in (gnu packages cran) and Bioconductor things in (gnu packages bioconductor), because it’s deliciously unsurprising. :) >> > + (synopsis "Decomposition of Bulk Expression with Single-Cell >> > Sequencing") >> >> Please use lowercase where it would be normally used. > > My mistake. I will take better care of this in the future. Thank you! Perhaps we could sprinkle some smarts over the CRAN importer to do this automatically, but with R packages we often have names of methods that should be upper case (like “Bayes*” or “SNPs”), so I have shied away from developing heuristics for that. Thanks for adding more R packages! -- Ricardo
Re: branch master updated: gnu: Add r-bisquerna.
Hi Ricardo, On Wed, 2020-09-09 at 18:04 +0200, Ricardo Wurmus wrote: > Hi Roel, > > > This is an automated email from the git hooks/post-receive script. > > > > roelj pushed a commit to branch master > > in repository guix. > > > > The following commit(s) were added to refs/heads/master by this > > push: > > new 0574446 gnu: Add r-bisquerna. > > 0574446 is described below > > > > commit 0574446be82ef54b925441e4283bf754a86918a9 > > Author: Roel Janssen > > AuthorDate: Wed Sep 9 17:02:55 2020 +0200 > > > > gnu: Add r-bisquerna. > > > > * gnu/packages/bioinformatics.scm (r-bisquerna): New variable. > > --- > > gnu/packages/bioinformatics.scm | 25 + > > 1 file changed, 25 insertions(+) > > > > diff --git a/gnu/packages/bioinformatics.scm > > b/gnu/packages/bioinformatics.scm > > index f8792ef..9f2fd86 100644 > > --- a/gnu/packages/bioinformatics.scm > > +++ b/gnu/packages/bioinformatics.scm > > @@ -7923,6 +7923,31 @@ manipulating genomic intervals and variables > > defined along a genome.") > > on Bioconductor or which replace R functions.") > > (license license:artistic2.0))) > > > > +(define-public r-bisquerna > > + (package > > + (name "r-bisquerna") > > + (version "1.0.4") > > + (source (origin > > +(method url-fetch) > > +(uri (cran-uri "BisqueRNA" version)) > > +(sha256 > > + (base32 > > + "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw > > 2" > > Why is this in (gnu packages bioinformatics) and not in (gnu packages > cran)? It seemed so "bioinformatics"-specific. But you're right, it's a CRAN package, so that may be a better fit. Shall I move it to CRAN? > > + (synopsis "Decomposition of Bulk Expression with Single-Cell > > Sequencing") > > Please use lowercase where it would be normally used. My mistake. I will take better care of this in the future. Kind regards, Roel Janssen
Re: branch master updated: gnu: Add r-bisquerna.
Hi Roel, > This is an automated email from the git hooks/post-receive script. > > roelj pushed a commit to branch master > in repository guix. > > The following commit(s) were added to refs/heads/master by this push: > new 0574446 gnu: Add r-bisquerna. > 0574446 is described below > > commit 0574446be82ef54b925441e4283bf754a86918a9 > Author: Roel Janssen > AuthorDate: Wed Sep 9 17:02:55 2020 +0200 > > gnu: Add r-bisquerna. > > * gnu/packages/bioinformatics.scm (r-bisquerna): New variable. > --- > gnu/packages/bioinformatics.scm | 25 + > 1 file changed, 25 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index f8792ef..9f2fd86 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -7923,6 +7923,31 @@ manipulating genomic intervals and variables defined > along a genome.") > on Bioconductor or which replace R functions.") > (license license:artistic2.0))) > > +(define-public r-bisquerna > + (package > + (name "r-bisquerna") > + (version "1.0.4") > + (source (origin > +(method url-fetch) > +(uri (cran-uri "BisqueRNA" version)) > +(sha256 > + (base32 > + "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2" Why is this in (gnu packages bioinformatics) and not in (gnu packages cran)? > + (synopsis "Decomposition of Bulk Expression with Single-Cell > Sequencing") Please use lowercase where it would be normally used. -- Ricardo
branch master updated: gnu: Add r-bisquerna.
This is an automated email from the git hooks/post-receive script.
roelj pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 0574446 gnu: Add r-bisquerna.
0574446 is described below
commit 0574446be82ef54b925441e4283bf754a86918a9
Author: Roel Janssen
AuthorDate: Wed Sep 9 17:02:55 2020 +0200
gnu: Add r-bisquerna.
* gnu/packages/bioinformatics.scm (r-bisquerna): New variable.
---
gnu/packages/bioinformatics.scm | 25 +
1 file changed, 25 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f8792ef..9f2fd86 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7923,6 +7923,31 @@ manipulating genomic intervals and variables defined
along a genome.")
on Bioconductor or which replace R functions.")
(license license:artistic2.0)))
+(define-public r-bisquerna
+ (package
+ (name "r-bisquerna")
+ (version "1.0.4")
+ (source (origin
+(method url-fetch)
+(uri (cran-uri "BisqueRNA" version))
+(sha256
+ (base32
+ "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"
+ (properties `((upstream-name . "BisqueRNA")))
+ (build-system r-build-system)
+ (propagated-inputs
+`(("r-biobase" ,r-biobase)
+ ("r-limsolve" ,r-limsolve)))
+ (home-page "https://www.biorxiv.org/content/10.1101/669911v1;)
+ (synopsis "Decomposition of Bulk Expression with Single-Cell Sequencing")
+ (description "This package provides tools to accurately estimate cell type
+abundances from heterogeneous bulk expression. A reference-based method
+utilizes single-cell information to generate a signature matrix and
+transformation of bulk expression for accurate regression based estimates.
+A marker-based method utilizes known cell-specific marker genes to measure
+relative abundances across samples.")
+ (license license:gpl3)))
+
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
