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s=key1; d=yhetil.org; t=1674997989; a=rsa-sha256; cv=none; b=gUQ50akpHHq4m3mWciTqZVV/mFbk1HjBQUkY2fShOP/93vTRKomCqUNpn8922Y+8i/I3IW ywwM0c0ampWTG+/JuHfi7hJ+bLOKNcHqDscPD8/TqIug4rlrs5/H3xRNh7vOTBezaMVpIg LXHcaUlQzC8cSvHNJKE/Ozc+OCcDXGb8LCO/LO9+Wb9MTAauOLBsTAZhldGO23Gp9EhLje dmMEtkDrJDxppX9WbSzGsU/bjNSx+vCsNVab2S8WIW1GatJO/tgIUJYRgZiqzSvV4xa+1A 5QF3fpIRVIJ4KaQKemZh252phstmMONLeluOjXwPJLhnAdYHWpPHTnYgcivN5A== Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=CmtEBItJ; 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-Scanner: scn0.migadu.com X-Migadu-Spam-Score: -2.48 X-Spam-Score: -2.48 X-Migadu-Queue-Id: 60A4C28116 X-TUID: YtbyN2veRxWw * gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.2. [source]: Add snippet to keep library name the same. [arguments]: Adjust the make-flags to find htslib. Enable the tests. Remove custom 'build-libraries phase, it is built by default now. Add a phase to symlink the shared library to a generic .so name. Don't override the 'install phase. Add a phase after 'install to create a pkg-config file. --- gnu/packages/bioinformatics.scm | 60 ++++++++++++++++++--------------- 1 file changed, 33 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5cea726f8e..fa0a6c0dd6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016, 2020, 2021 Roel Janssen -;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner +;;; Copyright © 2016-2023 Efraim Flashner ;;; Copyright © 2016, 2020, 2022 Marius Bakke ;;; Copyright © 2016, 2018 Raoul Bonnal ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice @@ -15640,7 +15640,7 @@ (define-public tbsp (define-public tabixpp (package (name "tabixpp") - (version "1.1.0") + (version "1.1.2") (source (origin (method git-fetch) (uri (git-reference @@ -15648,43 +15648,47 @@ (define-public tabixpp (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1k2a3vbq96ic4lw72iwp5s3mwwc4xhdffjj584yn6l9637q9j1yd")) + (base32 "00aqs147yn8zcvxims5njwxqsbnlbjv7lnmiwqy80bfdcbhljkqf")) (modules '((guix build utils))) (snippet #~(begin - (delete-file-recursively "htslib"))))) + (delete-file-recursively "htslib") + ;; Keep it named tabixpp. + (substitute* "Makefile" + (("libtabix") "libtabixpp")))))) (build-system gnu-build-system) - (inputs - (list bzip2 htslib xz zlib)) (arguments (list #:make-flags #~(list (string-append "CC=" #$(cc-for-target)) (string-append "CXX=" #$(cxx-for-target)) + (string-append "AR=" #$(ar-for-target)) "HTS_HEADERS=" - (string-append "HTS_LIB=" - (search-input-file %build-inputs - "/lib/libhts.a")) - "INCLUDES=") - #:tests? #f ; There are no tests to run. + "HTS_LIB=" + (string-append + "INCLUDES= -I" + (search-input-directory %build-inputs + "include/htslib")) + (string-append + "LIBPATH= -L. -L" + (dirname + (search-input-file %build-inputs + "/lib/libhts.a"))) + (string-append "PREFIX=" #$output) + "DESTDIR=") + #:test-target "test" #:phases #~(modify-phases %standard-phases (delete 'configure) ; There is no configure phase. - ;; Build shared and static libraries. - (add-after 'build 'build-libraries - (lambda* (#:key inputs #:allow-other-keys) - (invoke #$(cxx-for-target) - "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") - (invoke #$(ar-for-target) "rcs" "libtabixpp.a" "tabix.o"))) - (replace 'install + (add-after 'install 'symlink-shared-library + (lambda* (#:key outputs #:allow-other-keys) + (with-directory-excursion + (string-append (assoc-ref outputs "out") "/lib") + (symlink "libtabixpp.so.1" "libtabixpp.so")))) + (add-after 'install 'make-pkg-config-file (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib")) - (bin (string-append out "/bin"))) - (install-file "tabix++" bin) - (install-file "libtabixpp.so" lib) - (install-file "libtabixpp.a" lib) - (install-file "tabix.hpp" (string-append out "/include")) - (mkdir-p (string-append lib "/pkgconfig")) - (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc") + (pkgconfig (string-append out "/lib/pkgconfig"))) + (mkdir-p pkgconfig) + (with-output-to-file (string-append pkgconfig "/tabixpp.pc") (lambda _ (format #t "prefix=~a~@ exec_prefix=${prefix}~@ @@ -15692,12 +15696,14 @@ (define-public tabixpp includedir=${prefix}/include~@ ~@ ~@ - Name: libtabixpp~@ + Name: tabixpp~@ Version: ~a~@ Description: C++ wrapper around tabix project~@ Libs: -L${libdir} -ltabixpp~@ Cflags: -I${includedir}~%" out #$version))))))))) + (inputs + (list bzip2 curl htslib xz zlib)) (home-page "https://github.com/ekg/tabixpp") (synopsis "C++ wrapper around tabix project") (description "This is a C++ wrapper around the Tabix project which abstracts -- 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