Fix (vg) v1.65.0 with vcflib build [AI] HEAD master

1 files changed, 17 insertions, 2 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index a1de4b2..2037d3b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2658,6 +2658,20 @@ multiple sequence alignment.")
           (delete 'configure)
           (add-after 'unpack 'patch-source
             (lambda* (#:key inputs #:allow-other-keys)
+              ;; Add subdirectory include paths for system packages
+              (let ((extra-includes
+                     (string-join
+                      (list (search-input-directory inputs "/include/vcflib")
+                            (search-input-directory inputs "/include/fastahack")
+                            (search-input-directory inputs "/include/cairo")
+                            (search-input-directory inputs "/include/raptor2"))
+                      ":")))
+                (setenv "CPLUS_INCLUDE_PATH"
+                        (string-append extra-includes
+                                       ":" (or (getenv "CPLUS_INCLUDE_PATH") "")))
+                (setenv "C_INCLUDE_PATH"
+                        (string-append extra-includes
+                                       ":" (or (getenv "C_INCLUDE_PATH") ""))))
               (substitute* "Makefile"
                 ;; PKG_CONFIG_DEPS - use external vcflib and fastahack
                 (("cairo libzstd")
@@ -2689,8 +2703,9 @@ multiple sequence alignment.")
 
                 ((" \\$\\(FASTAHACK_DIR\\)/fastahack")
                  (string-append " " (search-input-file inputs "/bin/fastahack")))
-                (("\\+= \\$\\(OBJ_DIR\\)/Fasta\\.o")
-                 (string-append "+= " (search-input-file inputs "/lib/libfastahack.so")))
+                (("\\+= \\$\\(OBJ_DIR\\)/Fasta\\.o") "+=")
+                ;; Add fastahack to linker flags
+                (("-lvcflib") "-lvcflib -lfastahack -lsmithwaterman -lcairo")
 
                 ((" \\$\\(LIB_DIR\\)/libsnappy.a")
                  (string-append " " (search-input-file inputs "/lib/libsnappy.so")))