* [bug#32587] [PATCH] gnu: Add r-pore.
@ 2018-08-30 10:37 pimi
2018-09-03 15:22 ` Ricardo Wurmus
2018-09-11 14:54 ` pimi
0 siblings, 2 replies; 4+ messages in thread
From: pimi @ 2018-08-30 10:37 UTC (permalink / raw)
To: 32587; +Cc: pimi
gnu/packages/bioinformatics.scm (r-pore): New variable
---
gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#32587] [PATCH] gnu: Add r-pore.
2018-08-30 10:37 [bug#32587] [PATCH] gnu: Add r-pore pimi
@ 2018-09-03 15:22 ` Ricardo Wurmus
2018-09-11 14:54 ` pimi
1 sibling, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2018-09-03 15:22 UTC (permalink / raw)
To: MadalinIonel.Patrascu; +Cc: 32587
Hi,
thanks for the patch!
> +
> +(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.
> + (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.
> + (home-page "https://sourceforge.net/projects/rpore/files/")
Please use “https://sourceforge.net/projects/rpore”.
> + (synopsis "This R package enable visualisation of nanopore sequencing data")
Please use “Visualize 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.")
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.
> + (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:
https://github.com/mw55309/poRe_docs/issues/10
Could you please send an updated patch?
--
Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
* [bug#32587] [PATCH] gnu: Add r-pore.
2018-08-30 10:37 [bug#32587] [PATCH] gnu: Add r-pore pimi
2018-09-03 15:22 ` Ricardo Wurmus
@ 2018-09-11 14:54 ` pimi
2018-09-21 12:29 ` bug#32587: " Ludovic Courtès
1 sibling, 1 reply; 4+ messages in thread
From: pimi @ 2018-09-11 14:54 UTC (permalink / raw)
To: 32587; +Cc: pimi
gnu/packages/bioinformatics.scm (r-pore): New variable.
---
gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* bug#32587: [PATCH] gnu: Add r-pore.
2018-09-11 14:54 ` pimi
@ 2018-09-21 12:29 ` Ludovic Courtès
0 siblings, 0 replies; 4+ messages in thread
From: Ludovic Courtès @ 2018-09-21 12:29 UTC (permalink / raw)
To: pimi; +Cc: 32587-done
Hello,
pimi <madalinionel.patrascu@mdc-berlin.de> skribis:
> gnu/packages/bioinformatics.scm (r-pore): New variable.
[...]
> + (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’.
^ permalink raw reply [flat|nested] 4+ messages in thread
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2018-08-30 10:37 [bug#32587] [PATCH] gnu: Add r-pore pimi
2018-09-03 15:22 ` Ricardo Wurmus
2018-09-11 14:54 ` pimi
2018-09-21 12:29 ` bug#32587: " Ludovic Courtès
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