From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:53220) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1eHRhO-0007ey-NE for guix-patches@gnu.org; Wed, 22 Nov 2017 04:52:07 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1eHRhN-00084B-N2 for guix-patches@gnu.org; Wed, 22 Nov 2017 04:52:06 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:43174) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1eHRhN-000842-IP for guix-patches@gnu.org; Wed, 22 Nov 2017 04:52:05 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1eHRhN-0005QQ-9L for guix-patches@gnu.org; Wed, 22 Nov 2017 04:52:05 -0500 Subject: [bug#29392] [PATCH 06/11] gnu: metabat: Use scons-build-system. Resent-Message-ID: From: Arun Isaac Date: Wed, 22 Nov 2017 15:05:02 +0530 Message-Id: <20171122093507.6827-6-arunisaac@systemreboot.net> In-Reply-To: <20171122093507.6827-1-arunisaac@systemreboot.net> References: <20171122093507.6827-1-arunisaac@systemreboot.net> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 29392@debbugs.gnu.org * gnu/packages/bioinformatics.scm (metabat): Switch to scons-build-system. --- gnu/packages/bioinformatics.scm | 29 +++++++++-------------------- 1 file changed, 9 insertions(+), 20 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a8d7361ff..850c7462d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2016 Marius Bakke ;;; Copyright © 2016 Raoul Bonnal ;;; Copyright © 2017 Tobias Geerinckx-Rice +;;; Copyright © 2017 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -39,6 +40,7 @@ #:use-module (guix build-system python) #:use-module (guix build-system r) #:use-module (guix build-system ruby) + #:use-module (guix build-system scons) #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages autotools) @@ -3439,9 +3441,13 @@ form of assemblies or reads.") (base32 "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73")) (patches (search-patches "metabat-fix-compilation.patch")))) - (build-system gnu-build-system) + (build-system scons-build-system) (arguments - `(#:phases + `(#:scons-flags + (list (string-append "PREFIX=" (assoc-ref %outputs "out")) + (string-append "BOOST_ROOT=" (assoc-ref %build-inputs "boost"))) + #:tests? #f ;; Tests are run during the build phase. + #:phases (modify-phases %standard-phases (add-after 'unpack 'fix-includes (lambda _ @@ -3471,30 +3477,13 @@ form of assemblies or reads.") "/lib'")) ;; Do not distribute README. (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") "")) - #t)) - (delete 'configure) - (replace 'build - (lambda* (#:key inputs outputs #:allow-other-keys) - (mkdir (assoc-ref outputs "out")) - (zero? (system* "scons" - (string-append - "PREFIX=" - (assoc-ref outputs "out")) - (string-append - "BOOST_ROOT=" - (assoc-ref inputs "boost")) - "install")))) - ;; Check and install are carried out during build phase. - (delete 'check) - (delete 'install)))) + #t))))) (inputs `(("zlib" ,zlib) ("perl" ,perl) ("samtools" ,samtools) ("htslib" ,htslib) ("boost" ,boost))) - (native-inputs - `(("scons" ,scons))) (home-page "https://bitbucket.org/berkeleylab/metabat") (synopsis "Reconstruction of single genomes from complex microbial communities") -- 2.15.0