diff options
| author | Arun Isaac <arunisaac@systemreboot.net> | 2024-01-19 17:51:17 +0000 |
|---|---|---|
| committer | Arun Isaac <arunisaac@systemreboot.net> | 2024-01-19 18:04:39 +0000 |
| commit | 4987618368679f420dc89fda35a339d68d80761b (patch) | |
| tree | 7431ac4f16aac1b73a68e113c99e15bb53c3d39d | |
| parent | 15efd5a7f41c9282fd2a61f51df2765383ca4cb0 (diff) | |
gnu: wfmash: Update to 0.12.5.
* gnu/packages/bioinformatics.scm (wfmash): Update to 0.12.5.
(source): Use git-fetch. Update git repository URL.
(arguments): In check phase, symlink to "../source/data" and change wfmash
invocation arguments.
(home-page): Update URL.
Change-Id: I78f228f06a6a12e6904a58a12fd4201743e84d72
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 23 |
1 files changed, 12 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d0a3d94244..4198acecda 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 |