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authorEfraim Flashner2022-02-27 14:01:21 +0200
committerEfraim Flashner2022-02-27 14:01:21 +0200
commitf9d9127566c84b20efd8358b2e5cfa042a8729a8 (patch)
treef7e0ca9dedc06f4e2f049bd710e0f248d62eb84f /gn/packages/bioinformatics.scm
parent041f1402da12bd5493165f785a340e4d8682c814 (diff)
downloadguix-bioinformatics-f9d9127566c84b20efd8358b2e5cfa042a8729a8.tar.gz
gn: Add willowmap
Diffstat (limited to 'gn/packages/bioinformatics.scm')
-rw-r--r--gn/packages/bioinformatics.scm57
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)))