GNU bug report logs - #54635
[PATCH 0/5] Add wfmash

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From: Arun Isaac <arunisaac <at> systemreboot.net>
To: 54635 <at> debbugs.gnu.org
Cc: Arun Isaac <arunisaac <at> systemreboot.net>, Efraim Flashner <efraim <at> flashner.co.il>
Subject: [bug#54635] [PATCH 5/5] gnu: Add wfmash.
Date: Wed, 30 Mar 2022 14:53:13 +0530

* 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\"")
+              "<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

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