@@ 8,7 8,7 @@
;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2017, 2021, 2022, 2024 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
@@ 21402,15 21402,18 @@ based on the pairwise alignment of hidden Markov models (HMMs).")
(define-public wfmash
(package
(name "wfmash")
- (version "0.10.5")
+ (version "0.12.5")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/wfmash/releases/download/v"
- version "/wfmash-v" version ".tar.gz"))
+ ;; There are no release tarballs after version 0.10.5.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/waveygang/wfmash")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1jsvnnh14h3ir4l13qhmglhd25kzwvni9apgvr1lbikqwgrpkiq4"))
+ "1qh2chnwp7nqgp88afc4xzdkd21vh6cfqq73siqw7vc0qinqadm6"))
(snippet
#~(begin
(use-modules (guix build utils))
@@ 21436,8 21439,7 @@ based on the pairwise alignment of hidden Markov models (HMMs).")
(let ((samtools (search-input-file inputs "/bin/samtools")))
;; This is the easiest way to access the data
;; needed for the test suite.
- (symlink (string-append "../wfmash-v" #$version "/data")
- "data")
+ (symlink "../source/data" "data")
(and
;; This test takes 60 minutes on riscv64-linux.
#$@(if (not (target-riscv64?))
@@ 21529,8 21531,7 @@ based on the pairwise alignment of hidden Markov models (HMMs).")
(lambda _
(invoke "bin/wfmash"
"data/reads.255bps.fa.gz"
- "data/reads.255bps.fa.gz"
- "-X" "-w" "16")))
+ "-w" "16" "-s" "100" "-L")))
(invoke "head" "reads.255bps.paf"))))))))))
(inputs
(list atomic-queue
@@ 21547,7 21548,7 @@ 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")
+ (home-page "https://github.com/waveygang/wfmash")
(license license:expat)))
(define-public gdcm