diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 19 |
1 files changed, 14 insertions, 5 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a0f4738933..113bdc5675 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17220,11 +17220,13 @@ sequences to accelerate the alignment process.") ((".*smithwaterman.*") "") (("(pkg_check_modules\\(TABIXPP)" text) (string-append + "pkg_check_modules(WFA2 REQUIRED libwfa2)\n" "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n" "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n" text)) (("\\$\\{TABIXPP_LIBRARIES\\}" text) (string-append "${FASTAHACK_LIBRARIES} " + "${WFA2_LIBRARIES} " "${SMITHWATERMAN_LIBRARIES} " text))) (substitute* (find-files "." "\\.(h|c)(pp)?$") @@ -17244,9 +17246,10 @@ sequences to accelerate the alignment process.") pybind11 smithwaterman tabixpp - wfa2-lib xz zlib)) + (propagated-inputs + (list wfa2-lib)) (native-inputs `(("pkg-config" ,pkg-config) ;; Submodules. @@ -17262,7 +17265,6 @@ sequences to accelerate the alignment process.") "-DTABIXPP_LOCAL=OFF" "-DTABIX_FOUND=ON" "-DWFA_GITMODULE=OFF" - "-DWFA_LINK_LIBRARIES=-lwfa2cpp" (string-append "-DPKG_CONFIG_EXECUTABLE=" (search-input-file %build-inputs (string-append @@ -17270,7 +17272,7 @@ sequences to accelerate the alignment process.") #:tests? #f ; no tests #:phases #~(modify-phases %standard-phases - (add-after 'unpack 'find-wf2lib-headers + (add-after 'unpack 'find-wfa2lib-headers (lambda _ (setenv "CPLUS_INCLUDE_PATH" (string-append @@ -17297,7 +17299,14 @@ sequences to accelerate the alignment process.") (unpack "filevercmp-src" "contrib/filevercmp") (unpack "fsom-src" "contrib/fsom") (unpack "intervaltree-src" "contrib/intervaltree") - (unpack "multichoose-src" "contrib/multichoose"))))) + (unpack "multichoose-src" "contrib/multichoose")) + + ;; This is needed for downstream packages to allow building + ;; with GCC 11+. + (substitute* "contrib/intervaltree/IntervalTree.h" + (("#include <vector>" m) + (string-append m " +#include <limits> /* std::numeric_limits */")))))) ;; This pkg-config file is provided by other distributions. (add-after 'install 'install-pkg-config-file (lambda _ @@ -17313,7 +17322,7 @@ includedir=${prefix}/include~@ ~@ Name: vcflib~@ Version: ~a~@ -Requires: smithwaterman, fastahack, tabixpp~@ +Requires: libwfa2, smithwaterman, fastahack, tabixpp~@ Description: C++ library for parsing and manipulating VCF files~@ Libs: -L${libdir} -lvcflib~@ Cflags: -I${includedir}~%" |