diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 19 |
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"))) |