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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=systemreboot.net header.s=default header.b=mMPplOCd; dmarc=fail reason="SPF not aligned (relaxed)" header.from=systemreboot.net (policy=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-Spam-Score: 6.99 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=systemreboot.net header.s=default header.b=mMPplOCd; dmarc=fail reason="SPF not aligned (relaxed)" header.from=systemreboot.net (policy=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: 352598539 X-Spam-Score: 6.99 X-Migadu-Scanner: scn0.migadu.com X-TUID: PQIptvP14NZC * gnu/packages/bioinformatics.scm (vcflib)[source, arguments]: Rewrite using G-expressions. [arguments]: Do not return #t from custom phases. --- gnu/packages/bioinformatics.scm | 103 ++++++++++++++++---------------- 1 file changed, 51 insertions(+), 52 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ad69ca59cf..d74b8a0eb6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14548,27 +14548,27 @@ (define-public vcflib (base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh")) (modules '((guix build utils))) (snippet - '(begin - (substitute* "CMakeLists.txt" - ((".*fastahack.*") "") - ((".*smithwaterman.*") "") - (("(pkg_check_modules\\(TABIXPP)" text) - (string-append + #~(begin + (substitute* "CMakeLists.txt" + ((".*fastahack.*") "") + ((".*smithwaterman.*") "") + (("(pkg_check_modules\\(TABIXPP)" text) + (string-append "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n" "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n" text)) - (("\\$\\{TABIXPP_LIBRARIES\\}" text) - (string-append "${FASTAHACK_LIBRARIES} " - "${SMITHWATERMAN_LIBRARIES} " - text))) - (substitute* (find-files "." "\\.(h|c)(pp)?$") - (("\"SmithWatermanGotoh.h\"") "") - (("\"convert.h\"") "") - (("\"disorder.h\"") "") - (("Fasta.h") "fastahack/Fasta.h")) - (for-each delete-file-recursively - '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" - "libVCFH" "multichoose" "smithwaterman")))))) + (("\\$\\{TABIXPP_LIBRARIES\\}" text) + (string-append "${FASTAHACK_LIBRARIES} " + "${SMITHWATERMAN_LIBRARIES} " + text))) + (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")))))) (build-system cmake-build-system) (inputs (list bzip2 @@ -14589,39 +14589,39 @@ (define-public vcflib ("intervaltree-src" ,(package-source intervaltree)) ("multichoose-src" ,(package-source multichoose)))) (arguments - `(#:tests? #f ; no tests - #: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")))) - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (let ((unpack (lambda (source target) - (mkdir target) - (with-directory-excursion target - (if (file-is-directory? (assoc-ref inputs source)) - (copy-recursively (assoc-ref inputs source) ".") - (invoke "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) - (and - (unpack "filevercmp-src" "filevercmp") - (unpack "fsom-src" "fsom") - (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose"))))) - ;; This pkg-config file is provided by other distributions. - (add-after 'install 'install-pkg-config-file - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (pkgconfig (string-append out "/lib/pkgconfig"))) - (mkdir-p pkgconfig) - (with-output-to-file (string-append pkgconfig "/vcflib.pc") + (list #:tests? #f ; no tests + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'build-shared-library (lambda _ - (format #t "prefix=~a~@ + (substitute* "CMakeLists.txt" + (("vcflib STATIC") "vcflib SHARED")) + (substitute* "test/Makefile" + (("libvcflib.a") "libvcflib.so")))) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (mkdir target) + (with-directory-excursion target + (if (file-is-directory? (assoc-ref inputs source)) + (copy-recursively (assoc-ref inputs source) ".") + (invoke "tar" "xvf" + (assoc-ref inputs source) + "--strip-components=1")))))) + (and + (unpack "filevercmp-src" "filevercmp") + (unpack "fsom-src" "fsom") + (unpack "intervaltree-src" "intervaltree") + (unpack "multichoose-src" "multichoose"))))) + ;; This pkg-config file is provided by other distributions. + (add-after 'install 'install-pkg-config-file + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (pkgconfig (string-append out "/lib/pkgconfig"))) + (mkdir-p pkgconfig) + (with-output-to-file (string-append pkgconfig "/vcflib.pc") + (lambda _ + (format #t "prefix=~a~@ exec_prefix=${prefix}~@ libdir=${exec_prefix}/lib~@ includedir=${prefix}/include~@ @@ -14632,8 +14632,7 @@ (define-public vcflib Description: C++ library for parsing and manipulating VCF files~@ Libs: -L${libdir} -lvcflib~@ Cflags: -I${includedir}~%" - out ,version))) - #t)))))) + out #$version))))))))) (home-page "https://github.com/vcflib/vcflib/") (synopsis "Library for parsing and manipulating VCF files") (description "Vcflib provides methods to manipulate and interpret -- 2.35.1