diff mbox series

[bug#47010,09/10] gnu: r-shortread: Move to (gnu packages bioconductor).

Message ID 20210308175802.62517-9-zimon.toutoune@gmail.com
State Accepted
Headers show
Series Move some Bioconductor packages to (gnu packages bioconductor). | expand

Checks

Context Check Description
cbaines/submitting builds success
cbaines/comparison success View comparision
cbaines/git branch success View Git branch
cbaines/applying patch success View Laminar job
cbaines/issue success View issue

Commit Message

Simon Tournier March 8, 2021, 5:58 p.m. UTC 
* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
---
 gnu/packages/bioconductor.scm   | 43 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 43 ---------------------------------
 2 files changed, 43 insertions(+), 43 deletions(-)
diff mbox series

Patch

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4f4088db27..05077b422e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1845,6 +1845,49 @@  reports together for a particular project that can be viewed in a web
 browser.")
     (license license:artistic2.0)))
 
+(define-public r-shortread
+  (package
+    (name "r-shortread")
+    (version "1.48.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ShortRead" version))
+       (sha256
+        (base32
+         "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
+    (properties `((upstream-name . "ShortRead")))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-hwriter" ,r-hwriter)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-latticeextra" ,r-latticeextra)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (home-page "https://bioconductor.org/packages/ShortRead")
+    (synopsis "FASTQ input and manipulation tools")
+    (description
+     "This package implements sampling, iteration, and input of FASTQ files.
+It includes functions for filtering and trimming reads, and for generating a
+quality assessment report.  Data are represented as
+@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
+purposes.  The package also contains legacy support for early single-end,
+ungapped alignment formats.")
+    (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 186b051865..fda4516052 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,49 +7385,6 @@  includes software to
 ")
       (license license:cc0))))
 
-(define-public r-shortread
-  (package
-    (name "r-shortread")
-    (version "1.48.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ShortRead" version))
-       (sha256
-        (base32
-         "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
-    (properties `((upstream-name . "ShortRead")))
-    (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-hwriter" ,r-hwriter)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-latticeextra" ,r-latticeextra)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (home-page "https://bioconductor.org/packages/ShortRead")
-    (synopsis "FASTQ input and manipulation tools")
-    (description
-     "This package implements sampling, iteration, and input of FASTQ files.
-It includes functions for filtering and trimming reads, and for generating a
-quality assessment report.  Data are represented as
-@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
-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")