diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 90 |
1 files changed, 30 insertions, 60 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 7feadcd..7a7d0de 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2349,58 +2349,39 @@ sequences to accelerate the alignment process.") (properties '((tunable? . #t))) (license license:expat))) -(define-public vcflib-gn +(define-public vcflib (package - (name "vcflib-gn") - (version "1.0.14") - (source (local-file "/fast/pjotr/tmp/claude/factory/vcflib" - "vcflib-checkout" - #:recursive? #t)) + (name "vcflib") + (version "1.0.15") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vcflib/vcflib") + (commit (string-append "v" version)) + (recursive? #t))) ; some sources are included in the build + (file-name (git-file-name name version)) + (sha256 + (base32 + "0chpjd3g70jc0kwpf141z7rgm9i8pd8xxr1bfywyn15zfry774xa")))) (build-system cmake-build-system) (inputs - (list bzip2 - curl - htslib - fastahack - perl - python - pybind11 - smithwaterman - tabixpp - xz - zlib)) - (propagated-inputs - (list wfa2-lib/fixed)) - (native-inputs - (list pkg-config zig)) - (arguments (list - #:configure-flags - #~(list "-DZIG=ON" - "-DTABIXPP_LOCAL=OFF" - "-DTABIX_FOUND=ON" - "-DWFA_GITMODULE=OFF" - "-DBUILD_DOC=OFF") - #:tests? #f - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'find-wfa2lib-headers - (lambda _ - (setenv "CPLUS_INCLUDE_PATH" - (string-append - #$(this-package-input "wfa2-lib") - "/include/wfa2lib:" - (or (getenv "CPLUS_INCLUDE_PATH") ""))))) - (add-after 'unpack 'build-shared-library - (lambda _ - (substitute* "CMakeLists.txt" - (("vcflib STATIC") "vcflib SHARED")))) - (add-after 'build 'check - (lambda _ - ;; Skip pyvcflib and realign tests (require Python bindings) - (invoke "ctest" "--output-on-failure" - "--exclude-regex" "pyvcflib|realign"))) -))) + fastahack + htslib + pandoc ; for man pages + perl + python + python-pytest + pybind11 + ruby ; for man pages + smithwaterman + tabixpp + time ; for tests + wfa2-lib + xz + zig-0.15)) ; older versions of zig will not work + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "https://github.com/vcflib/vcflib/") (synopsis "Library for parsing and manipulating VCF files") (description "Vcflib provides methods to manipulate and interpret @@ -2661,8 +2642,6 @@ multiple sequence alignment.") license:zlib ; deps/sonLib/externalTools/cutest license:boost1.0)))) ; catch.hpp -;; vg-gn: uses vcflib-gn 1.0.14 which has canonicalize/getMaxReferencePos -;; merged back into Variant class (these were split out in 1.0.12). (define-public vg-gn (package (inherit vg) @@ -2828,7 +2807,7 @@ multiple sequence alignment.") snappy sparsehash tabixpp - vcflib-gn + vcflib zlib (list zstd "lib"))))) @@ -4682,15 +4661,6 @@ invariant (monomorphic) sites, which are essential for the correct computation of π and dxy in the face of missing data (i.e. always).") (license license:expat))) -(define-public wfa2-lib-static - (package - (inherit (static-package wfa2-lib)) - (name "wfa2-lib-static") - (arguments - (substitute-keyword-arguments (package-arguments wfa2-lib) - ((#:make-flags flags ''()) - #~(cons "CC_FLAGS+=-static" #$flags)))))) - (define-public r-rrbgen (package (name "r-rrbgen") |