Bump (vcflib) version to 1.0.15. Remove wfa2-lib-static package

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")