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dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=LuprAeUP; dmarc=none; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: E768933DCA X-Migadu-Scanner: scn1.migadu.com X-TUID: 2d/U7mR+ZQvm * gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.6. [source]: Adjust snippet to use unbundled wfa2-lib include directory. Also unbundle simde, wfa2-lib. Remove googletest from unbundle list, it is no longer in use. [inputs]: Add curl, simde, wfa2-lib. [native-inputs]: Add pybind11, pandoc when available. Add the sources for libvcfh. [arguments]: Adjust configure-flags to build without zig and to use the unbundled wfa2-lib. Adjust custom 'build-shared-library phase for changes in the source. Adjust custom 'unpack-submodule-sources for changes in the source. --- gnu/packages/bioinformatics.scm | 69 +++++++++++++++++++++++++-------- 1 file changed, 52 insertions(+), 17 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 05a07af7f3..c4eeb6d68f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16033,74 +16033,108 @@ (define-public fastahack (define-public vcflib (package (name "vcflib") - (version "1.0.3") + (version "1.0.6") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/vcflib/vcflib") - (commit (string-append "v" version)))) + (commit (string-append "v" version)) + (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh")) + (base32 "0zcs8j3vdajram53srvjmq353f3prqdbn8fvzja4412w4zay79fz")) (modules '((guix build utils))) (snippet #~(begin (substitute* "CMakeLists.txt" ((".*fastahack.*") "") ((".*smithwaterman.*") "") + ;; Also look for fastahack and smithwaterman since + ;; we've just unbundled them. (("(pkg_check_modules\\(TABIXPP)" text) (string-append "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n" "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n" text)) + ;; Also link vcflib to fastahack and smithwaterman. (("\\$\\{TABIXPP_LIBRARIES\\}" text) (string-append "${FASTAHACK_LIBRARIES} " "${SMITHWATERMAN_LIBRARIES} " - text))) + text)) + ;; Honor setting WFA_INCLUDE_DIRS and not look at + ;; PREFIX/include/wfa2lib. + (((string-append "\\$\\{CMAKE_INSTALL_PREFIX\\}/" + "\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}/wfa2lib")) + "${WFA_INCLUDE_DIRS}")) (substitute* (find-files "." "\\.(h|c)(pp)?$") (("\"SmithWatermanGotoh.h\"") "") (("\"convert.h\"") "") (("\"disorder.h\"") "") (("Fasta.h") "fastahack/Fasta.h")) - (for-each delete-file-recursively - '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" - "libVCFH" "multichoose" "smithwaterman")))))) + (substitute* "src/Variant.h" + (("wavefront/wfa.hpp") "wfa2lib/wavefront/wfa.hpp")) + (delete-file-recursively "src/simde") + (with-directory-excursion "contrib" + (for-each delete-file-recursively + '(;"c-progress-bar" + "fastahack" + "filevercmp" + "fsom" + "intervaltree" + "libVCFH" + "multichoose" + "smithwaterman" + "tabixpp" + "WFA2-lib"))))))) (build-system cmake-build-system) (inputs (list bzip2 + curl htslib fastahack perl python + simde smithwaterman tabixpp + wfa2-lib xz zlib)) (native-inputs `(("pkg-config" ,pkg-config) + ("pybind11" ,pybind11) + ,@(if (member (%current-system) + (package-transitive-supported-systems pandoc)) + `(("pandoc" ,pandoc)) + '()) ;; Submodules. - ;; This package builds against the .o files so we need to extract the source. + ;; Not all of these packages provide libraries to link against. ("filevercmp-src" ,(package-source filevercmp)) ("fsom-src" ,(package-source fsom)) ("intervaltree-src" ,(package-source intervaltree)) + ("libvcfh-src" ,(package-source libvcfh)) ("multichoose-src" ,(package-source multichoose)))) (arguments (list #:configure-flags - #~(list (string-append + #~(list "-DZIG=NO" + "-DWFA_GITMODULE=OFF" + (string-append "-DWFA_INCLUDE_DIRS=" + (search-input-directory %build-inputs + "include/wfa2lib")) + "-DTABIX_FOUND=ON" ; Default to found + (string-append "-DPKG_CONFIG_EXECUTABLE=" (search-input-file %build-inputs (string-append "/bin/" #$(pkg-config-for-target))))) - #:tests? #f ; no tests + #:tests? #f ; Tests need more configuring. #:phases #~(modify-phases %standard-phases (add-after 'unpack 'build-shared-library (lambda _ (substitute* "CMakeLists.txt" - (("vcflib STATIC") "vcflib SHARED")) - (substitute* "test/Makefile" - (("libvcflib.a") "libvcflib.so")))) + (("vcflib STATIC") "vcflib SHARED")))) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs native-inputs #:allow-other-keys) (let ((unpack (lambda (source target) @@ -16114,10 +16148,11 @@ (define-public vcflib source "--strip-components=1"))))))) (and - (unpack "filevercmp-src" "filevercmp") - (unpack "fsom-src" "fsom") - (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose"))))) + (unpack "filevercmp-src" "contrib/filevercmp") + (unpack "fsom-src" "contrib/fsom") + (unpack "intervaltree-src" "contrib/intervaltree") + (unpack "libvcfh-src" "contrib/libvcfh") + (unpack "multichoose-src" "contrib/multichoose"))))) ;; This pkg-config file is provided by other distributions. (add-after 'install 'install-pkg-config-file (lambda* (#:key outputs #:allow-other-keys) -- Efraim Flashner אפרים פלשנר GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted