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branch master updated: gnu: Add seqan 3.
From: |
guix-commits |
Subject: |
branch master updated: gnu: Add seqan 3. |
Date: |
Mon, 26 Jul 2021 06:27:58 -0400 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 3e5eff8 gnu: Add seqan 3.
3e5eff8 is described below
commit 3e5eff8c30f80d38c90c65d915bbd7359aca51a7
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Mon Jul 26 11:54:21 2021 +0200
gnu: Add seqan 3.
* gnu/packages/bioinformatics.scm (seqan): Rename this variable...
(seqan-2): ...to this.
(seqan): New variable for seqan3.
(flexbar)[native-inputs]: Update name for seqan 2.
---
gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++----------
1 file changed, 35 insertions(+), 11 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 91a3c1f..742b02c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3635,7 +3635,7 @@ results. The FASTX-Toolkit tools perform some of these
preprocessing tasks.")
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)
- ("seqan" ,seqan)))
+ ("seqan" ,seqan-2)))
(home-page "https://github.com/seqan/flexbar")
(synopsis "Barcode and adapter removal tool for sequencing platforms")
(description
@@ -6787,6 +6787,39 @@ writing files into the .sra format.")
(define-public seqan
(package
(name "seqan")
+ (version "3.0.3")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/seqan/seqan3/releases/"
+ "download/" version "/seqan3-"
+ version "-Source.tar.xz"))
+ (sha256
+ (base32
+ "1h2z0cvgidhkmh5xsbw75waqbrqbbv6kkrvb0b92xfh3gqpaiz22"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "ctest" "test" "--output-on-failure"))))))
+ (native-inputs
+ `(("bzip2" ,bzip2)
+ ("cereal" ,cereal)
+ ("zlib" ,zlib)))
+ (home-page "https://www.seqan.de")
+ (synopsis "Library for nucleotide sequence analysis")
+ (description
+ "SeqAn is a C++ library of efficient algorithms and data structures for
+the analysis of sequences with the focus on biological data. It contains
+algorithms and data structures for string representation and their
+manipulation, online and indexed string search, efficient I/O of
+bioinformatics file formats, sequence alignment, and more.")
+ (license license:bsd-3)))
+
+(define-public seqan-2
+ (package
+ (inherit seqan)
(version "2.4.0")
(source (origin
(method url-fetch)
@@ -6818,16 +6851,7 @@ writing files into the .sra format.")
(native-inputs
`(("source" ,source)
("tar" ,tar)
- ("xz" ,xz)))
- (home-page "https://www.seqan.de")
- (synopsis "Library for nucleotide sequence analysis")
- (description
- "SeqAn is a C++ library of efficient algorithms and data structures for
-the analysis of sequences with the focus on biological data. It contains
-algorithms and data structures for string representation and their
-manipulation, online and indexed string search, efficient I/O of
-bioinformatics file formats, sequence alignment, and more.")
- (license license:bsd-3)))
+ ("xz" ,xz)))))
(define-public seqan-1
(package (inherit seqan)
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