From: zimoun <zimon.toutoune@gmail.com>
To: 47010@debbugs.gnu.org
Cc: zimoun <zimon.toutoune@gmail.com>
Subject: [bug#47010] [PATCH 10/10] gnu: r-systempiper: Move to (gnu packages bioconductor).
Date: Mon, 8 Mar 2021 18:58:28 +0100 [thread overview]
Message-ID: <20210308175828.62579-1-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20210308175558.62461-1-zimon.toutoune@gmail.com>
* gnu/packages/bioinformatics.scm (r-systempiper): Move from here...
* gnu/packages/bioconductor.scm (r-systempiper): ...to here.
---
gnu/packages/bioconductor.scm | 54 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 54 ---------------------------------
2 files changed, 54 insertions(+), 54 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 05077b422e..d7be5e66a2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1888,6 +1888,60 @@ purposes. The package also contains legacy support for early single-end,
ungapped alignment formats.")
(license license:artistic2.0)))
+(define-public r-systempiper
+ (package
+ (name "r-systempiper")
+ (version "1.24.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "systemPipeR" version))
+ (sha256
+ (base32
+ "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
+ (properties `((upstream-name . "systemPipeR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-assertthat" ,r-assertthat)
+ ("r-batchtools" ,r-batchtools)
+ ("r-biostrings" ,r-biostrings)
+ ("r-deseq2" ,r-deseq2)
+ ("r-dot" ,r-dot)
+ ("r-edger" ,r-edger)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-go-db" ,r-go-db)
+ ("r-gostats" ,r-gostats)
+ ("r-iranges" ,r-iranges)
+ ("r-limma" ,r-limma)
+ ("r-magrittr" ,r-magrittr)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-rjson" ,r-rjson)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rsvg" ,r-rsvg)
+ ("r-shortread" ,r-shortread)
+ ("r-stringr" ,r-stringr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-yaml" ,r-yaml)
+ ("r-variantannotation" ,r-variantannotation)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/tgirke/systemPipeR")
+ (synopsis "Next generation sequencing workflow and reporting environment")
+ (description
+ "This R package provides tools for building and running automated
+end-to-end analysis workflows for a wide range of @dfn{next generation
+sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
+Important features include a uniform workflow interface across different NGS
+applications, automated report generation, and support for running both R and
+command-line software, such as NGS aligners or peak/variant callers, on local
+computers or compute clusters. Efficient handling of complex sample sets and
+experimental designs is facilitated by a consistently implemented sample
+annotation infrastructure.")
+ (license license:artistic2.0)))
+
(define-public r-geneplotter
(package
(name "r-geneplotter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fda4516052..072c0582be 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,60 +7385,6 @@ includes software to
")
(license license:cc0))))
-(define-public r-systempiper
- (package
- (name "r-systempiper")
- (version "1.24.3")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "systemPipeR" version))
- (sha256
- (base32
- "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
- (properties `((upstream-name . "systemPipeR")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-assertthat" ,r-assertthat)
- ("r-batchtools" ,r-batchtools)
- ("r-biostrings" ,r-biostrings)
- ("r-deseq2" ,r-deseq2)
- ("r-dot" ,r-dot)
- ("r-edger" ,r-edger)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-go-db" ,r-go-db)
- ("r-gostats" ,r-gostats)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-magrittr" ,r-magrittr)
- ("r-pheatmap" ,r-pheatmap)
- ("r-rjson" ,r-rjson)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rsvg" ,r-rsvg)
- ("r-shortread" ,r-shortread)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-yaml" ,r-yaml)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/tgirke/systemPipeR")
- (synopsis "Next generation sequencing workflow and reporting environment")
- (description
- "This R package provides tools for building and running automated
-end-to-end analysis workflows for a wide range of @dfn{next generation
-sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
-Important features include a uniform workflow interface across different NGS
-applications, automated report generation, and support for running both R and
-command-line software, such as NGS aligners or peak/variant callers, on local
-computers or compute clusters. Efficient handling of complex sample sets and
-experimental designs is facilitated by a consistently implemented sample
-annotation infrastructure.")
- (license license:artistic2.0)))
-
(define-public r-grohmm
(package
(name "r-grohmm")
--
2.30.1
next prev parent reply other threads:[~2021-03-08 18:54 UTC|newest]
Thread overview: 12+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-03-08 17:55 [bug#47010] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 01/10] gnu: r-genefilter: Move " zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 02/10] gnu: r-deseq2: " zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 03/10] gnu: r-dexseq: " zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 04/10] gnu: r-annotationforge: " zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 05/10] gnu: r-rbgl: " zimoun
2021-03-08 17:57 ` [bug#47010] [PATCH 06/10] gnu: r-gseabase: " zimoun
2021-03-08 17:58 ` [bug#47010] [PATCH 07/10] gnu: r-category: " zimoun
2021-03-08 17:58 ` [bug#47010] [PATCH 08/10] gnu: r-gostats: " zimoun
2021-03-08 17:58 ` [bug#47010] [PATCH 09/10] gnu: r-shortread: " zimoun
2021-03-08 17:58 ` zimoun [this message]
2021-03-12 13:54 ` bug#47010: [PATCH 00/10] Move some Bioconductor packages " Ricardo Wurmus
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=20210308175828.62579-1-zimon.toutoune@gmail.com \
--to=zimon.toutoune@gmail.com \
--cc=47010@debbugs.gnu.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.