diff mbox series

[bug#47171,09/10] gnu: r-rsamtools: Move to (gnu packages bioconductor).

Message ID 20210315180904.8346-9-zimon.toutoune@gmail.com
State Accepted
Headers show
Series Move some Bioconductor packages to (gnu packages bioconductor). | expand

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Commit Message

Simon Tournier March 15, 2021, 6:09 p.m. UTC 
* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...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 2b7d65023d..c659bdd09e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2147,6 +2147,49 @@  reports together for a particular project that can be viewed in a web
 browser.")
     (license license:artistic2.0)))
 
+(define-public r-rsamtools
+  (package
+    (name "r-rsamtools")
+    (version "2.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Rsamtools" version))
+              (sha256
+               (base32
+                "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
+    (properties
+     `((upstream-name . "Rsamtools")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-zlib
+           (lambda _
+             (substitute* "DESCRIPTION"
+               (("zlibbioc, ") ""))
+             (substitute* "NAMESPACE"
+               (("import\\(zlibbioc\\)") ""))
+             #t)))))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bitops" ,r-bitops)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
+    (synopsis "Interface to samtools, bcftools, and tabix")
+    (description
+     "This package provides an interface to the @code{samtools},
+@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
+Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
+tab-delimited (tabix) files.")
+    (license license:expat)))
+
 (define-public r-shortread
   (package
     (name "r-shortread")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 415210085e..05805d1a8b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,49 +7691,6 @@  including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-rsamtools
-  (package
-    (name "r-rsamtools")
-    (version "2.6.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "Rsamtools" version))
-              (sha256
-               (base32
-                "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
-    (properties
-     `((upstream-name . "Rsamtools")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-system-zlib
-           (lambda _
-             (substitute* "DESCRIPTION"
-               (("zlibbioc, ") ""))
-             (substitute* "NAMESPACE"
-               (("import\\(zlibbioc\\)") ""))
-             #t)))))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bitops" ,r-bitops)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
-    (synopsis "Interface to samtools, bcftools, and tabix")
-    (description
-     "This package provides an interface to the @code{samtools},
-@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
-Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
-tab-delimited (tabix) files.")
-    (license license:expat)))
-
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")