fix vcflib

1 files changed, 62 insertions, 4 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index a4671fd..00ec739 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2319,9 +2319,44 @@ in-memory footprint at the cost of packing and unpacking.")
                             odgi-x86-64-v4)))
     (properties `((tunable? . #f)))))
 
-(define-public vcflib
+;; wfa2-lib from Guix fails with GCC 13+ due to missing <cstdint>.
+(define-public wfa2-lib/fixed
   (package
-    (name "vcflib")
+    (inherit wfa2-lib)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'fix-cstdint
+                 (lambda _
+                   (substitute* "bindings/cpp/WFAligner.hpp"
+                     (("#include <string>" m)
+                      (string-append m "\n#include <cstdint>")))
+                   ;; C headers need <stdint.h>
+                   (substitute* (find-files "." "\\.(h|c)$")
+                     (("#include <stdlib.h>" m)
+                      (string-append m "\n#include <stdint.h>")))))
+               (add-after 'install 'install-pkg-config-file
+                 (lambda _
+                   (let ((pkgconfig (string-append #$output "/lib/pkgconfig")))
+                     (mkdir-p pkgconfig)
+                     (with-output-to-file (string-append pkgconfig "/libwfa2.pc")
+                       (lambda _
+                         (format #t "prefix=~a~@
+exec_prefix=${prefix}~@
+libdir=${exec_prefix}/lib~@
+includedir=${prefix}/include/wfa2lib~@
+~@
+Name: libwfa2~@
+Version: ~a~@
+Description: Wavefront alignment algorithm library~@
+Libs: -L${libdir} -lwfa2 -lwfa2cpp~@
+Cflags: -I${includedir}~%"
+                                 #$output
+                                 #$(package-version wfa2-lib))))))))))))
+
+(define-public vcflib-gn
+  (package
+    (name "vcflib-gn")
     (version "1.0.12")
     (source
      (origin
@@ -2370,7 +2405,7 @@ in-memory footprint at the cost of packing and unpacking.")
            xz
            zlib))
     (propagated-inputs
-     (list wfa2-lib))
+     (list wfa2-lib/fixed))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ;; Submodules.
@@ -2433,7 +2468,7 @@ in-memory footprint at the cost of packing and unpacking.")
 prefix=~a~@
 exec_prefix=${prefix}~@
 libdir=${exec_prefix}/lib~@
-includedir=${prefix}/include~@
+includedir=${prefix}/include/vcflib~@
 ~@
 Name: vcflib~@
 Version: ~a~@
@@ -5053,6 +5088,29 @@ annotated in the reference.")
     (license license:gpl2)))
 
 
+(define-public r-dendextendrcpp
+  (package
+    (name "r-dendextendrcpp")
+    (version "0.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/talgalili/dendextendRcpp/archive/refs/tags/"
+			   version version ".tar.gz"))
+       (sha256
+        (base32
+         "1vhqy8licl2pkzar4aag0q5fhnb3fdch8acyjh9445ia42z01z9c"))))
+    (build-system r-build-system)
+    (arguments
+     (list #:tests? #f))  ;; tests fail and seem to require data
+    (propagated-inputs
+     (list r-rcpp
+	   r-rcpparmadillo))
+    (home-page "https://github.com/talgalili/dendextendRcpp")
+    (synopsis "A dendrogram object in R are is a list structure with attributes in its nodes and leaves.")
+    (description "A dendrogram object in R are is a list structure with attributes in its nodes and leaves.")
+    (license license:gpl3)))
+
 (define-public r-dendextend
   (package
     (name "r-dendextend")