From: zimoun <zimon.toutoune@gmail.com>
To: 45399@debbugs.gnu.org
Subject: [bug#45399] [PATCH 09/10] gnu: r-gqtlstats: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:34 +0100 [thread overview]
Message-ID: <20201223180635.58647-10-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com>
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
---
gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 47 ---------------------------------
2 files changed, 47 insertions(+), 47 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ff9e26bbde..a3dd93e763 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9308,6 +9308,53 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
by Ernst and Kellis.")
(license license:artistic2.0)))
+(define-public r-gqtlbase
+ (package
+ (name "r-gqtlbase")
+ (version "1.21.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gQTLBase" version))
+ (sha256
+ (base32
+ "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
+ (properties `((upstream-name . "gQTLBase")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ ;; This is an upstream bug.
+ (add-after 'unpack 'fix-imports
+ (lambda _
+ (substitute* "NAMESPACE"
+ ((".*maxffmode.*") "")
+ (("importFrom\\(ff,.*") "import(ff)\n"))
+ #t)))))
+ (propagated-inputs
+ `(("r-batchjobs" ,r-batchjobs)
+ ("r-bbmisc" ,r-bbmisc)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-bit" ,r-bit)
+ ("r-doparallel" ,r-doparallel)
+ ("r-ff" ,r-ff)
+ ("r-ffbase" ,r-ffbase)
+ ("r-foreach" ,r-foreach)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/gQTLBase")
+ (synopsis "Infrastructure for eQTL, mQTL and similar studies")
+ (description
+ "The purpose of this package is to simplify the storage and interrogation
+of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
+and more.")
+ (license license:artistic2.0)))
+
(define-public r-gqtlstats
(package
(name "r-gqtlstats")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 76236929de..bc483e6f13 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10549,53 +10549,6 @@ views. High-level plots include sequence fragment length, edge-linked
interval to data view, mismatch pileup, and several splicing summaries.")
(license license:artistic2.0)))
-(define-public r-gqtlbase
- (package
- (name "r-gqtlbase")
- (version "1.21.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "gQTLBase" version))
- (sha256
- (base32
- "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
- (properties `((upstream-name . "gQTLBase")))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- ;; This is an upstream bug.
- (add-after 'unpack 'fix-imports
- (lambda _
- (substitute* "NAMESPACE"
- ((".*maxffmode.*") "")
- (("importFrom\\(ff,.*") "import(ff)\n"))
- #t)))))
- (propagated-inputs
- `(("r-batchjobs" ,r-batchjobs)
- ("r-bbmisc" ,r-bbmisc)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-bit" ,r-bit)
- ("r-doparallel" ,r-doparallel)
- ("r-ff" ,r-ff)
- ("r-ffbase" ,r-ffbase)
- ("r-foreach" ,r-foreach)
- ("r-genomicfiles" ,r-genomicfiles)
- ("r-genomicranges" ,r-genomicranges)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/gQTLBase")
- (synopsis "Infrastructure for eQTL, mQTL and similar studies")
- (description
- "The purpose of this package is to simplify the storage and interrogation
-of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
-and more.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.29.2
next prev parent reply other threads:[~2020-12-23 18:07 UTC|newest]
Thread overview: 14+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-12-23 18:03 [bug#45399] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2020-12-23 18:06 ` zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 01/10] gnu: r-sushi: Move " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 02/10] gnu: r-gwascat: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 03/10] gnu: r-gviz: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 04/10] gnu: r-gqtlstats: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 05/10] gnu: r-ldblock: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 06/10] gnu: r-erma: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 07/10] gnu: r-homo-sapiens: " zimoun
2020-12-23 18:06 ` [bug#45399] [PATCH 08/10] gnu: r-snpstats: " zimoun
2020-12-23 18:06 ` zimoun [this message]
2020-12-23 18:06 ` [bug#45399] [PATCH 10/10] gnu: r-ggbio: " zimoun
2020-12-29 16:42 ` bug#45399: [PATCH 00/10] Move some Bioconductor packages " Ricardo Wurmus
2020-12-30 9:13 ` [bug#45399] " zimoun
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