diff options
| -rw-r--r-- | gn/packages/pangenome.scm | 76 |
1 files changed, 76 insertions, 0 deletions
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm index b605fd1..f0a3cc7 100644 --- a/gn/packages/pangenome.scm +++ b/gn/packages/pangenome.scm @@ -34,6 +34,10 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages time) + #:use-module (gnu packages check) + #:use-module (gnu packages haskell-xyz) + #:use-module (gnu packages ruby) + #:use-module (gnu packages zig) #:use-module (gn packages pangenome-rust) #:use-module (gnu packages python-xyz)) @@ -783,6 +787,77 @@ sequences using wfmash, seqwish, smoothxg, and gfaffix.") (prepend jemalloc) (delete "libdeflate"))))) +;; wfa2-lib v2.3.6 with cmake build, pkg-config support +(define-public wfa2-lib/cmake + (package + (name "wfa2-lib") + (version "2.3.6") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smarco/WFA2-lib") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0hfgq09r0ndrsa2jwy9wkg8p7xzgvclbj5ysp73bawwkgwpgfhy4")))) + (build-system cmake-build-system) + (native-inputs + (list pkg-config time)) + (arguments + (list + #:configure-flags + #~(list "-DCMAKE_BUILD_TYPE=RelWithDebInfo"))) + (home-page "https://github.com/smarco/WFA2-lib") + (synopsis "Wavefront alignment algorithm library") + (description "The wavefront alignment (WFA) algorithm is an exact +gap-affine algorithm that takes advantage of homologous regions between the +sequences to accelerate the alignment process.") + (properties '((tunable? . #t))) + (license license:expat))) + +(define-public vcflib + (let ((commit "b118a9bfd99b07da9d40d0bd8b3c2bdc4523b568") + (revision "1")) + (package + (name "vcflib") + (version (git-version "1.0.15" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vcflib/vcflib") + (commit commit) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1qgipn1vgkipd36hcm10mz0rg6h04azng2hp5zsjrpr4k1dh1fdr")))) + (build-system cmake-build-system) + (inputs + (list fastahack + htslib + pandoc + perl + python + python-pytest + pybind11 + ruby + smithwaterman + tabixpp + time + wfa2-lib/cmake + xz + zig-0.15)) + (native-inputs + (list pkg-config)) + (home-page "https://github.com/vcflib/vcflib/") + (synopsis "Library for parsing and manipulating VCF files") + (description "Vcflib provides methods to manipulate and interpret +sequence variation as it can be described by VCF. It is both an API for parsing +and operating on records of genomic variation as it can be described by the VCF +format, and a collection of command-line utilities for executing complex +manipulations on VCF files.") + (license license:expat)))) + (define-public pangenomes (package (name "pangenomes") @@ -817,6 +892,7 @@ sequences using wfmash, seqwish, smoothxg, and gfaffix.") seqwish smoothxg vcfbub + vcflib wally wfmash)) (home-page "https://github.com/pangenome") |