Re-add vcflib package

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")