From patchwork Tue Apr 26 12:46:31 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38909 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 4F1B727BBEA; Tue, 26 Apr 2022 13:56:27 +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 BB7EC27BBE9 for ; Tue, 26 Apr 2022 13:56:26 +0100 (BST) Received: from localhost ([::1]:44082 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njKjx-0006yg-Qt for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 08:56:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43890) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njKav-0007B8-7l for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43661) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njKat-0007VA-O3 for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njKat-0004kY-LD for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55125] [PATCH 1/9] gnu: tabixpp: Use G-expressions. References: <20220426124426.16845-1-arunisaac@systemreboot.net> In-Reply-To: <20220426124426.16845-1-arunisaac@systemreboot.net> Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 12:47:03 +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=B55125.165097720917484 (code B ref 55125); Tue, 26 Apr 2022 12:47:03 +0000 Received: (at 55125) by debbugs.gnu.org; 26 Apr 2022 12:46:49 +0000 Received: from localhost ([127.0.0.1]:37539 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKae-0004XW-Vc for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:49 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36274) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKac-0004UR-4o for 55125@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:47 -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: 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:In-Reply-To:References:List-Id:List-Help:List-Unsubscribe: List-Subscribe:List-Post:List-Owner:List-Archive; bh=fhX6aMVFl7JG7gS21iWUKApvWWjTppiI+ftfyQbJEOo=; b=dEBZo8Fq7HxOLPVve/gTNWfoPn 0unTFkyNm/mxoXDFT5XWeIsMKncVXUwSghik37vhIQHqV66VgxVT+IhNDXt94k0HCQOjApLk2WrmL zCrWzt6uUm2DOi0v+TZWkrV8dTd/D0y7VSsiVAOkfSw+fV7EGFszJVn2GPg+CXrLYjC8g0kBRIK8s wgNDY8ivTyEsr8xJpyz4kOGRAuqn/VcbQXtJf75/G3fMzcOo5Uw7DKEvvLxqWgKI7UIVT9/Jx0EFU v8W3yJYzQONV5dQEcQbLFTPQ/BmOcgbh+O/CZC/hYWSXO3vvMEWL3fEXb0pW8gENl3TKTuCqYWxS1 GClWnzMg==; 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 1njKaZ-000HJN-Bb; Tue, 26 Apr 2022 18:16:43 +0530 From: Arun Isaac Date: Tue, 26 Apr 2022 18:16:31 +0530 Message-Id: <20220426124639.17159-1-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.35.1 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 (tabixpp)[source]: Reindent. [arguments]: Use search-input-file and search-input-directory. [source, arguments]: Rewrite using G-expressions. Do not return #t from snippets and custom phases. --- gnu/packages/bioinformatics.scm | 80 ++++++++++++++++----------------- 1 file changed, 39 insertions(+), 41 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 40ccba247c..774da809d8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14264,49 +14264,48 @@ (define-public tabixpp (name "tabixpp") (version "1.1.0") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/tabixpp") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1k2a3vbq96ic4lw72iwp5s3mwwc4xhdffjj584yn6l9637q9j1yd")) - (modules '((guix build utils))) - (snippet - `(begin - (delete-file-recursively "htslib") #t)))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1k2a3vbq96ic4lw72iwp5s3mwwc4xhdffjj584yn6l9637q9j1yd")) + (modules '((guix build utils))) + (snippet + #~(begin + (delete-file-recursively "htslib"))))) (build-system gnu-build-system) (inputs (list htslib zlib)) (arguments - `(#:tests? #f ; There are no tests to run. - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - ;; The build phase needs overriding the location of htslib. - (replace 'build - (lambda* (#:key inputs #:allow-other-keys) - (let ((htslib-ref (assoc-ref inputs "htslib"))) - (invoke "make" - (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") - (string-append "INCLUDES= -I" htslib-ref "/include/htslib") - "HTS_HEADERS=" ; No need to check for headers here. - (string-append "LIBPATH=-L. -L" htslib-ref "/include")) - (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") - (invoke "ar" "rcs" "libtabixpp.a" "tabix.o")))) - (replace 'install - (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") - (lambda _ - (format #t "prefix=~a~@ + (list #:tests? #f ; There are no tests to run. + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + ;; The build phase needs overriding the location of htslib. + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (invoke "make" + (string-append "HTS_LIB=" (search-input-file inputs "/lib/libhts.a")) + (string-append "INCLUDES= -I" (search-input-directory inputs "/include/htslib")) + "HTS_HEADERS=" ; No need to check for headers here. + (string-append "LIBPATH=-L. -L" (search-input-directory inputs "/include"))) + (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") + (invoke "ar" "rcs" "libtabixpp.a" "tabix.o"))) + (replace 'install + (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") + (lambda _ + (format #t "prefix=~a~@ exec_prefix=${prefix}~@ libdir=${exec_prefix}/lib~@ includedir=${prefix}/include~@ @@ -14317,8 +14316,7 @@ (define-public tabixpp Description: C++ wrapper around tabix project~@ Libs: -L${libdir} -ltabixpp~@ Cflags: -I${includedir}~%" - out ,version))) - #t)))))) + out #$version))))))))) (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