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From: Arun Isaac <arunisaac@systemreboot.net>
To: Efraim Flashner <efraim@flashner.co.il>,
	Maxime Devos <maximedevos@telenet.be>
Cc: 54635@debbugs.gnu.org, Arun Isaac <arunisaac@systemreboot.net>
Subject: [bug#54635] [PATCH v2 5/5] gnu: Add wfmash.
Date: Thu, 31 Mar 2022 12:58:49 +0530	[thread overview]
Message-ID: <20220331072849.22417-5-arunisaac@systemreboot.net> (raw)
In-Reply-To: <YkRBijIJ16QKrr5G@3900XT>

* 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





  parent reply	other threads:[~2022-03-31  7:31 UTC|newest]

Thread overview: 28+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2022-03-30  9:19 [bug#54635] [PATCH 0/5] Add wfmash Arun Isaac
2022-03-30  9:23 ` [bug#54635] [PATCH 1/5] gnu: gsl: Force bootstrap when cross-compiling to riscv64-linux Arun Isaac
2022-03-30  9:23   ` [bug#54635] [PATCH 2/5] gnu: htslib: Add bzip2 and xz to inputs Arun Isaac
2022-03-30  9:23   ` [bug#54635] [PATCH 3/5] gnu: atomic-queue: Run tests correctly Arun Isaac
2022-03-30  9:23   ` [bug#54635] [PATCH 4/5] gnu: atomic-queue: Do not depend on boost when cross-compiling Arun Isaac
2022-03-30 11:49     ` Maxime Devos
2022-03-31  7:24       ` Arun Isaac
2022-03-30  9:23   ` [bug#54635] [PATCH 5/5] gnu: Add wfmash Arun Isaac
2022-03-30 11:33   ` [bug#54635] [PATCH 1/5] gnu: gsl: Force bootstrap when cross-compiling to riscv64-linux Maxime Devos
2022-03-31  6:14     ` Arun Isaac
2022-03-30 11:36   ` Maxime Devos
2022-03-30 11:39     ` Efraim Flashner
2022-03-31  6:33       ` Arun Isaac
2022-03-31 11:29         ` Maxime Devos
2022-03-31 12:35         ` Efraim Flashner
2022-03-31  7:28       ` [bug#54635] [PATCH v2 " Arun Isaac
2022-03-31  7:28       ` [bug#54635] [PATCH v2 2/5] gnu: htslib: Add bzip2 and xz to inputs Arun Isaac
2022-03-31  7:28       ` [bug#54635] [PATCH v2 3/5] gnu: atomic-queue: Run tests correctly Arun Isaac
2022-03-31  7:28       ` [bug#54635] [PATCH v2 4/5] gnu: atomic-queue: Do not look for boost when cross-compiling Arun Isaac
2022-03-31  7:28       ` Arun Isaac [this message]
2022-03-31 11:34         ` [bug#54635] [PATCH v2 5/5] gnu: Add wfmash Maxime Devos
2022-03-31 12:18           ` Efraim Flashner
2022-03-31 13:07             ` Maxime Devos
2022-03-31 13:09               ` Efraim Flashner
2022-03-31 13:31               ` bug#54635: " Efraim Flashner
2022-04-01  7:40                 ` [bug#54635] " Arun Isaac
2022-04-01  9:39                   ` Maxime Devos
2022-04-04 18:01                     ` Arun Isaac

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