diff options
-rw-r--r-- | gnu/packages/bioinformatics.scm | 82 |
1 files changed, 82 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 31205c473a..cf09fc3add 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")) |