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gnu: Add kraken2. 

* gnu/packages/bioinformatics.scm (kraken2): New variable.
master
Ricardo Wurmus 2021-04-22 08:14:51 +02:00
parent f3eb13df69
commit 92032d8081
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1 changed files with 82 additions and 0 deletions
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gnu/packages/bioinformatics.scm
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@ -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"))