From patchwork Tue Apr 26 12:46:37 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38910 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 920DC27BBEA; Tue, 26 Apr 2022 13:56:37 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 08DDB27BBE9 for ; Tue, 26 Apr 2022 13:56:37 +0100 (BST) Received: from localhost ([::1]:44888 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njKk8-0007WK-4s for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 08:56:36 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43900) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njKax-0007Ca-9U for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43666) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njKax-0007Vd-0J for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njKaw-0004n0-Sf for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55125] [PATCH 7/9] gnu: vcflib: Use G-expressions. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 12:47:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55125 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55125@debbugs.gnu.org Cc: Arun Isaac Received: via spool by 55125-submit@debbugs.gnu.org id=B55125.165097721617886 (code B ref 55125); Tue, 26 Apr 2022 12:47:06 +0000 Received: (at 55125) by debbugs.gnu.org; 26 Apr 2022 12:46:56 +0000 Received: from localhost ([127.0.0.1]:37551 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKal-0004dt-Ri for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:56 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36286) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKac-0004VS-DO for 55125@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:48 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:MIME-Version: References:In-Reply-To:Message-Id:Date:Subject:Cc:To:From:Sender:Reply-To: Content-Type:Content-ID:Content-Description:Resent-Date:Resent-From: Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=1Mk35J4+8LbnUr5pc/Ygl355xCPWdPfUFUgXBpduoac=; b=mMPplOCd9k4WMuhBt500I4vdoF Uz52UKDzt3603iWTx00wPjKMvRX2QH+FigGxdEMElBBkQVCGsWSMBwfUxKM+3eujbqP1/myW2wmz1 rlUeZ2BfFlCxM/187nwPx2r8gdWUh2gQYa9q8gUT4HptYfgrkD2ieSNZoc9UvjdMMMLtzKQLsdGYp 3rho7RUizUNm+IlPCNE9QR+yN3CBmqEexUrScWd8QDWJ2l8/Av2wwv6/6oqq4XLWr5narawFM7VuU oDc2s5HOAM0KTaJUSyGuxap/wIhrBQK8LJBzUED8b35nAWliGeNocHXnhfyiTbYIGEAXxY6vatsns JBx+LifQ==; Received: from [192.168.2.1] (port=53438 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.95) (envelope-from ) id 1njKaa-000HJN-Gw; Tue, 26 Apr 2022 18:16:44 +0530 From: Arun Isaac Date: Tue, 26 Apr 2022 18:16:37 +0530 Message-Id: <20220426124639.17159-7-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.35.1 In-Reply-To: <20220426124639.17159-1-arunisaac@systemreboot.net> References: <20220426124639.17159-1-arunisaac@systemreboot.net> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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