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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=systemreboot.net header.s=default header.b=BZHEFGwQ; dmarc=fail reason="SPF not aligned (relaxed)" header.from=systemreboot.net (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 6.33 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=systemreboot.net header.s=default header.b=BZHEFGwQ; dmarc=fail reason="SPF not aligned (relaxed)" header.from=systemreboot.net (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 4A4D52976C X-Spam-Score: 6.33 X-Migadu-Scanner: scn0.migadu.com X-TUID: uMaMt6ybexiC * gnu/packages/bioinformatics.scm (wfmash): New variable. --- gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2f6f3efb66..500ba4ac60 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16107,3 +16107,54 @@ (define-public ccwl @acronym{EDSL, Embedded Domain Specific Language} in the Scheme programming language.") (license license:gpl3+))) + +(define-public wfmash + (package + (name "wfmash") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/wfmash/releases/download/v" + version "/wfmash-v" version ".tar.gz")) + (sha256 + (base32 + "031cm1arpfckvihb28vlk69mirpnmlag81zcscfba1bac58wvr7c")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Unbundle atomic-queue. + (delete-file-recursively "src/common/atomic_queue") + (substitute* "src/align/include/computeAlignments.hpp" + (("\"common/atomic_queue/atomic_queue.h\"") + "")))))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + ;; Remove compiler flags and checks specific to x86 when not + ;; targeting it. + ,@(if (target-x86-64?) + '() + '((add-after 'unpack 'remove-x86-specific-compile-flags + (lambda _ + (substitute* (find-files "." "CMakeLists\\.txt") + (("-mcx16") "") + (("-march=native") "")) + (substitute* "src/common/dset64.hpp" + (("!__x86_64__") "0"))))))))) + (inputs + (list atomic-queue + gsl + htslib + jemalloc + zlib)) + (synopsis "Base-accurate DNA sequence aligner") + (description "@code{wfmash} is a DNA sequence read mapper based on mash +distances and the wavefront alignment algorithm. It is a fork of MashMap that +implements base-level alignment via the wflign tiled wavefront global +alignment algorithm. It completes MashMap with a high-performance alignment +module capable of computing base-level alignments for very large sequences.") + (home-page "https://github.com/ekg/wfmash") + (license license:expat))) -- 2.34.0