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| author | Arun Isaac <arunisaac@systemreboot.net> | 2022-03-31 12:58:49 +0530 |
|---|---|---|
| committer | Efraim Flashner <efraim@flashner.co.il> | 2022-03-31 16:14:53 +0300 |
| commit | 1ca9d9e1942b674cd2a4ce55ebfebc4485870366 (patch) | |
| tree | b33c73b3d2276c0d4b1d121981b050303be4acd1 /gnu | |
| parent | 8524904e082464b7eb0c10037613b73da4d4df5e (diff) | |
| download | guix-patches-1ca9d9e1942b674cd2a4ce55ebfebc4485870366.tar guix-patches-1ca9d9e1942b674cd2a4ce55ebfebc4485870366.tar.gz | |
gnu: Add wfmash.
* gnu/packages/bioinformatics.scm (wfmash): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9c7ef41cc1..7a7f2f722e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16124,3 +16124,48 @@ workflows from concise descriptions in ccwl. It is implemented as an @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")) + (snippet + #~(begin + (use-modules (guix build utils)) + ;; Unbundle atomic-queue. + (delete-file-recursively "src/common/atomic_queue") + (substitute* "src/align/include/computeAlignments.hpp" + (("\"common/atomic_queue/atomic_queue.h\"") + "<atomic_queue/atomic_queue.h>")) + ;; Remove compiler optimizations. + (substitute* (find-files "." "CMakeLists\\.txt") + (("-mcx16 ") "") + (("-march=native ") "")) + ;; Allow building on architectures other than x86_64. + (substitute* "src/common/dset64.hpp" + (("!__x86_64__") "0")))))) + (build-system cmake-build-system) + (arguments + (list #:tests? #f)) ; no tests + (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))) |