diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 60 |
1 files changed, 60 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 4c2f8cf..67b2270 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -3138,3 +3138,63 @@ from a VCF. In particular, pixy facilitates the use of VCFs containing invariant (monomorphic) sites, which are essential for the correct computation of π and dxy in the face of missing data (i.e. always).") (license license:expat))) + +(define-public wfa2-lib + (let ((commit "af6be887614e8bb4e2b6e8c4e500705a978bd513") ; 14 April 2022 + (revision "1")) + (package + (name "wfa2-lib") + (version (git-version "2.1" revision commit)) ; As seen in ./VERSION + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smarco/WFA2-lib") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "09gsmks4dzmfscklb60m6gcsvsd9r6jywf10633dpcsfsdcvmzaw")) + (snippet + #~(begin + (use-modules ((guix build utils))) + (substitute* "Makefile" + (("^CC=") "CC:=") + (("^CPP=") "CPP:=") + (("-march=native") "")))))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; No tests. + #:parallel-build? #f ; Race condition in Makefile. + #:modules '((guix build gnu-build-system) + (guix build utils) + (srfi srfi-26)) + #:make-flags + #~(list (string-append "CC=" #$(cc-for-target)) + (string-append "CPP=" #$(cxx-for-target))) + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; No configure script. + ;; -flto breaks align_benchmark. + (replace 'build + (lambda* (#:key (make-flags '()) #:allow-other-keys) + (apply invoke "make" "all" make-flags))) + (replace 'install + (lambda _ + (for-each + (cut install-file <> (string-append #$output "/bin")) + (find-files "bin")) + (for-each + (cut install-file <> (string-append #$output "/lib")) + (find-files "lib"))))))) + (home-page "https://github.com/smarco/WFA2-lib") + (synopsis "Wavefront alignment algorithm library") + (description "The @acronym{wavefront alignment, WFA} algorithm is an exact +gap-affine algorithm that takes advantage of homologous regions between the +sequences to accelerate the alignment process. Unlike to traditional dynamic +programming algorithms that run in quadratic time, the WFA runs in time +@code{O(ns+s^2)}, proportional to the sequence length @code{n} and the alignment +score @code{s}, using @code{O(s^2)} memory. Moreover, the WFA algorithm +exhibits simple computational patterns that the modern compilers can +automatically vectorize for different architectures without adapting the code.") + (properties '((tunable? . #t))) + (license license:expat)))) |