[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
branch master updated: gnu: Add kraken2.
From: |
guix-commits |
Subject: |
branch master updated: gnu: Add kraken2. |
Date: |
Thu, 22 Apr 2021 02:33:24 -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 92032d8 gnu: Add kraken2.
92032d8 is described below
commit 92032d8081713d56c3bcf84c7e15b55a22a1e0a3
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Thu Apr 22 08:14:51 2021 +0200
gnu: Add kraken2.
* gnu/packages/bioinformatics.scm (kraken2): New variable.
---
gnu/packages/bioinformatics.scm | 82 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 82 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 31205c4..cf09fc3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -144,6 +144,7 @@
#:use-module (gnu packages tls)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
+ #:use-module (gnu packages wget)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (srfi srfi-1)
@@ -15061,6 +15062,87 @@ signaling, and more. It continues to be evolved and
expanded by an
international community.")
(license license:lgpl2.1+)))
+(define-public kraken2
+ (package
+ (name "kraken2")
+ (version "2.1.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/DerrickWood/kraken2")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0h7a7vygd7y5isbrnc6srwq6xj1rmyd33pm8mmcgfkmlxlg5vkg3"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #false ; there are none
+ #:make-flags (list "-C" "src"
+ (string-append "KRAKEN2_DIR="
+ (assoc-ref %outputs "out") "/bin"))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'install 'install-scripts
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((bin (string-append (assoc-ref outputs "out") "/bin"))
+ (scripts (find-files "scripts" ".*"))
+ (replacements `(("KRAKEN2_DIR" . ,bin)
+ ("VERSION" . ,,version))))
+ (mkdir-p bin)
+ (substitute* scripts
+ (("#####=([^=]+)=#####" _ key)
+ (or (assoc-ref replacements key)
+ (error (format #false "unknown key: ~a~%" key)))))
+ (substitute* "scripts/kraken2"
+ (("compression_program = \"bzip2\"")
+ (string-append "compression_program = \""
+ (which "bzip2")
+ "\""))
+ (("compression_program = \"gzip\"")
+ (string-append "compression_program = \""
+ (which "gzip")
+ "\"")))
+ (substitute* '("scripts/download_genomic_library.sh"
+ "scripts/download_taxonomy.sh"
+ "scripts/16S_gg_installation.sh"
+ "scripts/16S_silva_installation.sh"
+ "scripts/16S_rdp_installation.sh")
+ (("wget") (which "wget")))
+ (substitute* "scripts/mask_low_complexity.sh"
+ (("which") (which "which")))
+ (substitute* '("scripts/mask_low_complexity.sh"
+ "scripts/download_genomic_library.sh"
+ "scripts/16S_silva_installation.sh")
+ (("sed -e ")
+ (string-append (which "sed") " -e ")))
+ (substitute* '("scripts/rsync_from_ncbi.pl"
+ "scripts/16S_rdp_installation.sh"
+ "scripts/16S_silva_installation.sh"
+ "scripts/16S_gg_installation.sh"
+ "scripts/download_taxonomy.sh"
+ "scripts/download_genomic_library.sh")
+ (("gunzip") (which "gunzip")))
+ (for-each (lambda (script)
+ (chmod script #o555)
+ (install-file script bin))
+ scripts)))))))
+ (inputs
+ `(("gzip" ,gzip)
+ ("perl" ,perl)
+ ("sed" ,sed)
+ ("wget" ,wget)
+ ("which" ,which)))
+ (home-page "https://github.com/DerrickWood/kraken2")
+ (synopsis "Taxonomic sequence classification system")
+ (description "Kraken is a taxonomic sequence classifier that assigns
+taxonomic labels to DNA sequences. Kraken examines the k-mers within a query
+sequence and uses the information within those k-mers to query a
+database. That database maps k-mers to the lowest common ancestor (LCA) of all
+genomes known to contain a given k-mer.")
+ (license license:expat)))
+
(define-public r-signac
(let ((commit "e0512d348adeda4a3f23a2e8f56d1fe09840e03c")
(revision "1"))
[Prev in Thread] |
Current Thread |
[Next in Thread] |
- branch master updated: gnu: Add kraken2.,
guix-commits <=