[PATCH] gnu: Add r-pore.

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4 participants
  • Ludovic Courtès
  • pimi
  • Ricardo Wurmus
  • Ricardo Wurmus
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Somebody
Submitted by
pimi
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pimi wrote 7 years ago
(address . guix-patches@gnu.org)(name . pimi)(address . madalinionel.patrascu@mdc-berlin.de)
20180830103703.10473-1-madalinionel.patrascu@mdc-berlin.de
gnu/packages/bioinformatics.scm (r-pore): New variable
---
gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)

Toggle diff (37 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 22a00894c..0605e4564 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13558,3 +13558,30 @@ reference transcripts provided in a annotation file (also in GTF/GFF3 format).
(list
license:expat ;license for gffcompare
license:artistic2.0))))) ;license for gclib
+
+(define-public r-pore
+ (package
+ (name "r-pore")
+ (version "0.24")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://sourceforge.net/projects/rpore/files/"version"/poRe_"version".tar.gz"))
+ (sha256
+ (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv"))))
+ (properties `((upstream-name . "poRe")))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-rhdf5" ,r-rhdf5)
+ ("r-shiny" ,r-shiny)
+ ("r-svdialogs" ,r-svdialogs)
+ ("r-data-table" ,r-data-table)
+ ("r-bit64" ,r-bit64)))
+ (home-page "https://sourceforge.net/projects/rpore/files/")
+ (synopsis "This R package enable visualisation of nanopore sequencing data")
+ (description
+ "The Oxford Nanopore MinION is a revolutionary sequencer with a unique model of data
+delivery, requiring novel tools for the novice user. This package enables
+organisation and visualisation of MinION data.")
+ (license license:gpl3)))
--
2.17.1
Ricardo Wurmus wrote 7 years ago
(address . MadalinIonel.Patrascu@mdc-berlin.de)(address . 32587@debbugs.gnu.org)
idjpnxu38sq.fsf@bimsb-sys02.mdc-berlin.net
Hi,

thanks for the patch!

Toggle quote (11 lines)
> +
> +(define-public r-pore
> + (package
> + (name "r-pore")
> + (version "0.24")
> + (source
> + (origin
> + (method url-fetch)
> + (uri (string-append
> + "https://sourceforge.net/projects/rpore/files/"version"/poRe_"version".tar.gz"))

Please use mirror://sourceforge/ here.

Toggle quote (11 lines)
> + (sha256
> + (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv"))))
> + (properties `((upstream-name . "poRe")))
> + (build-system r-build-system)
> + (native-inputs
> + `(("r-rhdf5" ,r-rhdf5)
> + ("r-shiny" ,r-shiny)
> + ("r-svdialogs" ,r-svdialogs)
> + ("r-data-table" ,r-data-table)
> + ("r-bit64" ,r-bit64)))

Are you sure these should be native-inputs? They probably should be
propagated inputs, because they should be installed together with the
“r-pore” package.

Please also sort these inputs alphabetically.

Toggle quote (2 lines)

Toggle quote (2 lines)
> + (synopsis "This R package enable visualisation of nanopore sequencing data")

Please use “Visualize Nanopore sequencing data”.

Toggle quote (5 lines)
> + (description
> + "The Oxford Nanopore MinION is a revolutionary sequencer with a unique model of data
> +delivery, requiring novel tools for the novice user. This package enables
> +organisation and visualisation of MinION data.")

Please try to avoid marketing terms such as “revolutionary”, “unique”,
“novel” etc. Could you try to come up with a description that better
describes the features of the poRe package?

Here’s a draft:

This package provides graphical user interfaces to organize and
visualize Nanopore sequencing data.

Toggle quote (2 lines)
> + (license license:gpl3)))

I don’t think this is correct. The DESCRIPTION file says “BSD”, but
fails to state the variant. I have opened an issue about this here:


Could you please send an updated patch?

--
Ricardo
pimi wrote 7 years ago
(address . 32587@debbugs.gnu.org)(name . pimi)(address . madalinionel.patrascu@mdc-berlin.de)
20180911145432.3477-1-madalinionel.patrascu@mdc-berlin.de
gnu/packages/bioinformatics.scm (r-pore): New variable.
---
gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)

Toggle diff (38 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f6410c3ca..49ed19535 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13699,3 +13699,31 @@ are highly customizable. Currently, it is possible to plot: bigwig, bed (many
options), bedgraph, links (represented as arcs), and Hi-C matrices.
pyGenomeTracks can make plots with or without Hi-C data.")
(license license:gpl3+)))
+
+(define-public r-pore
+ (package
+ (name "r-pore")
+ (version "0.24")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "mirror://sourceforge/projects/rpore/files/"version"/poRe_"version".tar.gz"))
+ (sha256
+ (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv"))))
+ (properties `((upstream-name . "poRe")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bit64" ,r-bit64)
+ ("r-data-table" ,r-data-table)
+ ("r-rhdf5" ,r-rhdf5)
+ ("r-shiny" ,r-shiny)
+ ("r-svdialogs" ,r-svdialogs)))
+ (home-page "https://sourceforge.net/projects/rpore")
+ (synopsis "Visualize Nanopore sequencing data")
+ (description
+ "This package provides graphical user interfaces to organize and visualize Nanopore
+sequencing data.")
+ ;;license unclear https://github.com/mw55309/poRe_docs/issues/10
+ (license license:bsd-3)))
--
2.17.1
Ricardo Wurmus wrote 6 years ago
control message for bug #32587
(address . control@debbugs.gnu.org)
165d3e227e9.630907442054671123.2886074654087780988@zoho.com
owner 32587 !
Ludovic Courtès wrote 6 years ago
Re: [bug#32587] [PATCH] gnu: Add r-pore.
(name . pimi)(address . madalinionel.patrascu@mdc-berlin.de)(address . 32587-done@debbugs.gnu.org)
87worf11bf.fsf@gnu.org
Hello,

pimi <madalinionel.patrascu@mdc-berlin.de> skribis:

Toggle quote (2 lines)
> gnu/packages/bioinformatics.scm (r-pore): New variable.

[...]

Toggle quote (3 lines)
> + (string-append
> + "mirror://sourceforge/projects/rpore/files/"version"/poRe_"version".tar.gz"))

I fixed the URL, clarified the comment about the license, and committed.

Thanks!

Ludo’.
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