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| -rw-r--r-- | gn/packages/bioinformatics.scm | 57 |
1 files changed, 57 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 9e94f96..12595ab 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -3039,3 +3039,60 @@ input sequences, pick syncmers from hpc-compressed sequences, connect syncmers with an edge if they are adjacent in a read, unitigify and homopolymer decompress. Suggested input is PacBio HiFi/CCS reads.") (license license:expat))) + +;; TODO: Unbundle bloom, meryl. +(define-public willowmap + (package + (name "willowmap") + (version "2.03") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/marbl/Winnowmap") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "152650bljmdm9f1nmi4xbpxs9583faijba9i8gkp3qz76pzcvbfh")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* "ext/meryl/src/utility/src/utility/system.C" + ;; This was removed in glibc-2.32. + ((".*sys/sysctl\\.h.*") "")))))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; No tests. + #:make-flags + #~(list "OSVERSION=5.15") + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; No configure script. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each (lambda (file) + (install-file file (string-append out "/bin"))) + (find-files "bin")))))))) + (inputs + (list zlib)) + (native-inputs + (list perl + which)) + (home-page "https://github.com/marbl/Winnowmap") + (synopsis "Long read / genome alignment software") + (description + "Winnowmap is a long-read mapping algorithm optimized for mapping ONT and +PacBio reads to repetitive reference sequences. Winnowmap implements a novel +weighted minimizer sampling algorithm (>=v1.0). This optimization was motivated +by the need to avoid masking of frequently occurring k-mers during the seeding +stage in an efficient manner, and achieve better mapping accuracy in complex +repeats (e.g., long tandem repeats) of the human genome. Using weighted +minimizers, Winnowmap down-weights frequently occurring k-mers, thus reducing +their chance of getting selected as minimizers.") + (supported-systems '("x86_64-linux")) + ;; minimap2 based code is expat, as is bloom. + ;; Meryl is mix bsd-3, expat and public-domain. + ;; Rest of the code is public domain. + (license license:expat))) |