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branch master updated: gnu: Add centrifuge.
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guix-commits |
Subject: |
branch master updated: gnu: Add centrifuge. |
Date: |
Fri, 30 Sep 2022 11:01:14 -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 729ce5fcf8 gnu: Add centrifuge.
729ce5fcf8 is described below
commit 729ce5fcf8a8ea412a91fa2ff01c0ad07c355424
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Sep 30 16:56:20 2022 +0200
gnu: Add centrifuge.
* gnu/packages/bioinformatics.scm (centrifuge): New variable.
---
gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ca341a45a7..c5b47eedf5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8464,6 +8464,46 @@ BLAST, KEGG, GenBank, MEDLINE and GO.")
;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
(license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
+(define-public centrifuge
+ (package
+ (name "centrifuge")
+ (version "1.0.4")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/DaehwanKimLab/centrifuge.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "167610gbz1rrh6ir3j7jcmhzg3x5msn7x7a3dpv7wmwdndnnqvg0"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:tests? #false ; no check target
+ #:make-flags
+ #~(list (string-append "prefix=" #$output))
+ #:phases
+ '(modify-phases %standard-phases
+ (delete 'configure))))
+ (inputs (list python-wrapper))
+ (native-inputs
+ (list pandoc perl ;for documentation
+ which))
+ (home-page "https://github.com/DaehwanKimLab/centrifuge/")
+ (synopsis "Classifier for metagenomic sequences")
+ (description "Centrifuge is a microbial classification engine that enables
+rapid, accurate and sensitive labeling of reads and quantification of species
+on desktop computers. The system uses an indexing scheme based on the
+@dfn{Burrows-Wheeler transform} (BWT) and the @dfn{Ferragina-Manzini} (FM)
+index, optimized specifically for the metagenomic classification problem.
+Centrifuge requires a relatively small index (4.7 GB for all complete
+bacterial and viral genomes plus the human genome) and classifies sequences at
+very high speed, allowing it to process the millions of reads from a typical
+high-throughput DNA sequencing run within a few minutes.")
+ (license license:gpl3+)))
+
(define-public bio-vcf
(package
(name "bio-vcf")
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