From patchwork Sun Jan 29 13:12:34 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Efraim Flashner X-Patchwork-Id: 46516 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 7E5A027BBE9; Sun, 29 Jan 2023 13:13:26 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS 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 D3A9127BBF0 for ; Sun, 29 Jan 2023 13:13:22 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pM7UW-000370-5A; Sun, 29 Jan 2023 08:13:04 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pM7UV-00035C-0h for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pM7UU-0007jW-Mr for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pM7UU-0003Zi-HK for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61148] [PATCH 1/5] gnu: intervaltree: Update to 0.1-1.aa59377. Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 29 Jan 2023 13:13:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61148 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61148@debbugs.gnu.org Cc: Efraim Flashner Received: via spool by 61148-submit@debbugs.gnu.org id=B61148.167499797113678 (code B ref 61148); Sun, 29 Jan 2023 13:13:02 +0000 Received: (at 61148) by debbugs.gnu.org; 29 Jan 2023 13:12:51 +0000 Received: from localhost ([127.0.0.1]:42423 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UI-0003YX-J1 for submit@debbugs.gnu.org; Sun, 29 Jan 2023 08:12:50 -0500 Received: from mail-ej1-f51.google.com ([209.85.218.51]:36557) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UG-0003YC-UK for 61148@debbugs.gnu.org; Sun, 29 Jan 2023 08:12:49 -0500 Received: by mail-ej1-f51.google.com with SMTP id kt14so24986212ejc.3 for <61148@debbugs.gnu.org>; Sun, 29 Jan 2023 05:12:48 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:from:to:cc:subject:date :message-id:reply-to; bh=3AsLpxDeV25H4eZflOnf1flD4aeJ9FI3BgMFmWDDlug=; b=EjwAfPk9xNKk9YUpAX4Ol5Mcs4VUcewtY9IG2ZoZUBrlwl06EF5aHPbXuDPe9tmOrg KUC6HSjalxKhICUkGFNd3dhS1iWFgtMC0Q0DeaKEzsEueXEEfSNToQ0gtqdtEDt0F9bR EKKWmiGg+E+/SXM2oAHOG3vvsjFH/DaV5+jT626YdZdpHr3TODoYelGg/cO1u8W3LS1v LhtLrTQ3HDGk+bcThsf5uk+9vfoINcy7O5d4t6VPhRwBLZQqG9pODTkhEY/9g6oOrq2G vDeaak/j/AirL8QDtmsblZTAKo4TudkhH9Dv722dalVacaqKELOtoXdgEnEgtpjR9HGT z/OA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:x-gm-message-state:from :to:cc:subject:date:message-id:reply-to; bh=3AsLpxDeV25H4eZflOnf1flD4aeJ9FI3BgMFmWDDlug=; b=to79b4MOVZuq3DTDr4JHR+mVyTTKVimTf6BJVg1G2yknrKLNuFm9i6v9fZxRtY2OYm 1Bv3sFkbsU5+fk2j81y1Yc0jvdFZOX/hrJVIP3mSdlWqldBNaEtkC4y+2hKfG1wejafu JEbGjAGuAELzmHQG828jFuF+c7oIknHH4iPi1o851rC0R7PDh2EEuhb98UZJEjuJKEuw KRQmK3VBGQAgvT+Mwp6bsgazbCFUcc4/IQxtqzaZY6itUTN7I3bqElUkVOmMuj0Tms9A aS6YJGoTX+o2HELhAuDMHuRi6p3fcDUTW/GY4oWe6GwY9hSRwkrrdNoN8k7djCwkBMsW yWuQ== X-Gm-Message-State: AO0yUKUJLHDDFwkrpFdYhO3eIhEB6yqIJL69w68F+VdFpD9EB4Dr2EDu huGKkS7827BSOTU9dGNOiZRfHfv9GfB1+Q== X-Google-Smtp-Source: AK7set9/fOHjDjpF2SCWoxboNc4vY45+Sp2dGReO9Cd+JFE6rViJLB2OegdQtdrQOswfGRZHQu/8iw== X-Received: by 2002:a17:906:171a:b0:878:69bc:2a8 with SMTP id c26-20020a170906171a00b0087869bc02a8mr12646640eje.69.1674997961717; Sun, 29 Jan 2023 05:12:41 -0800 (PST) Received: from localhost ([141.226.15.115]) by smtp.gmail.com with ESMTPSA id gn19-20020a1709070d1300b008512e1379dbsm5429176ejc.171.2023.01.29.05.12.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 29 Jan 2023 05:12:41 -0800 (PST) From: Efraim Flashner Date: Sun, 29 Jan 2023 15:12:34 +0200 Message-Id: <4fd1568af1aa4bafb18a1efbcdfd084ca6b18711.1674997469.git.efraim@flashner.co.il> X-Mailer: git-send-email 2.39.1 In-Reply-To: References: 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (intervaltree): Update to 0.1-1.aa59377. [arguments]: Fix cross-compiling. --- gnu/packages/bioinformatics.scm | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8c75607a65..5cea726f8e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13632,10 +13632,10 @@ (define-public gffcompare license:artistic2.0))))) ;license for gclib (define-public intervaltree - (let ((commit "b90527f9e6d51cd36ecbb50429e4524d3a418ea5")) + (let ((commit "aa5937755000f1cd007402d03b6f7ce4427c5d21")) (package (name "intervaltree") - (version (git-version "0.0.0" "1" commit)) + (version (git-version "0.1" "1" commit)) (source (origin (method git-fetch) @@ -13644,15 +13644,18 @@ (define-public intervaltree (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0rgv6q5fl4x5d74n6p5wvdna6zmbdbqpb4jqqh6vq3670gn08xad")))) + (base32 "0p9aphy6sc01dg67xzqpnhvjmk21xa380bpfbkz24a23s6krhjwl")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; No tests. + (list + #:tests? #f ; No tests. #:make-flags - ,#~(list (string-append "PREFIX=" #$output) "DESTDIR=\"\"") + #~(list (string-append "PREFIX=" #$output) + (string-append "CXX=" #$(cxx-for-target)) + "DESTDIR=") #:phases - (modify-phases %standard-phases - (delete 'configure)))) ; There is no configure phase. + #~(modify-phases %standard-phases + (delete 'configure)))) ; There is no configure phase. (home-page "https://github.com/ekg/intervaltree") (synopsis "Minimal C++ interval tree implementation") (description "An interval tree can be used to efficiently find a set of From patchwork Sun Jan 29 13:12:35 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Efraim Flashner X-Patchwork-Id: 46513 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 7EE4D27BBEB; Sun, 29 Jan 2023 13:13:13 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 EDDC427BBE9 for ; Sun, 29 Jan 2023 13:13:08 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pM7UW-00037F-Ew; Sun, 29 Jan 2023 08:13:04 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pM7UV-00035J-8n for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pM7UV-0007jb-0l for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pM7UU-0003Zq-TD for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61148] [PATCH 2/5] gnu: tabixpp: Update to 1.1.2. Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 29 Jan 2023 13:13:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61148 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61148@debbugs.gnu.org Cc: Efraim Flashner Received: via spool by 61148-submit@debbugs.gnu.org id=B61148.167499797513709 (code B ref 61148); Sun, 29 Jan 2023 13:13:02 +0000 Received: (at 61148) by debbugs.gnu.org; 29 Jan 2023 13:12:55 +0000 Received: from localhost ([127.0.0.1]:42427 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UN-0003Z2-0x for submit@debbugs.gnu.org; Sun, 29 Jan 2023 08:12:55 -0500 Received: from mail-ej1-f49.google.com ([209.85.218.49]:34451) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UH-0003YF-Nr for 61148@debbugs.gnu.org; Sun, 29 Jan 2023 08:12:51 -0500 Received: by mail-ej1-f49.google.com with SMTP id k4so19463895eje.1 for <61148@debbugs.gnu.org>; Sun, 29 Jan 2023 05:12:49 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:from:to:cc:subject:date :message-id:reply-to; bh=1PCUhE/L0M2H2dena0RELGjSYOKbvsFFB/n1rVIN0Dk=; b=CmtEBItJNxtIRamsPWVO4tGfbskXd/gJJ74MERBd9De2oFVCob4864nag2xc14kgcn cOOWa4wicKrB0eYEzoNp45O4p0Dh6WnfbUpA27PuJB7WlDOGaNfBQzr/qOIzHmJR9nSY HrCSZTiQhHl7BiCjn788ncRaBzjBGepQB/cpflRYrQqLz/V1TNdGIONkwNfFRjBMB91T 15s2Xqf1RyJJbeSyGvri1vQ9PId6YCy9a8/WxT4GY2XOL9a+I8foIWj+5mtEu591Wauh eoQqoEY34GYzj0btXSymUoC26UNhypi6j+I862JMjqN74A4zpXc2ys3DPyKPyPtxokcu m6zw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:x-gm-message-state:from :to:cc:subject:date:message-id:reply-to; bh=1PCUhE/L0M2H2dena0RELGjSYOKbvsFFB/n1rVIN0Dk=; b=a/pEWyuEFx0oeT/mt0VHauCvuhsg1PWZpKiPquZ/iplyEVwGU2fOSi3QKBNYZnQgWN JBBmxPun8g+Z01ynzO0mI1LXm8A3RMomPv3rvl48x4ZgjI1CgEa2X8HltDPUYiJpuTqA udy6y3/KcWKUFMc8qzsAKt6PmpAneSPmX3JC/dC8uIwHtC0B60sRgXfin7OrL8ya3ath +Cdzi1qYEBGtO8bXksxJ/9RwP6Ki9BRpOK+PSThhEpXcWTr45onN8OpSedxH3d9Q/kkn yvEM5VNfzMGgFmCfEG4vF0IagCBpZc1eVVdzgjfaQk2M03e75v4VgI8MENWrpRm5Y9jV /wKQ== X-Gm-Message-State: AO0yUKWdKcdIo9JN0WQeQQhhaseDIk3rlBVLzUzhEXuiFpFPDaEcJQB7 1sQzewor7qb6sO4Xwd1mC8eGTWt1ULsX+g== X-Google-Smtp-Source: AK7set97CuT3g56W/01ftZ+48zYLgZnhXeSerTTOqIk1GioU/QgbWKPeMdDnScIKJwUuzIBToGQy3g== X-Received: by 2002:a17:906:9d18:b0:860:5723:a5e5 with SMTP id fn24-20020a1709069d1800b008605723a5e5mr8190663ejc.69.1674997963866; Sun, 29 Jan 2023 05:12:43 -0800 (PST) Received: from localhost ([141.226.15.115]) by smtp.gmail.com with ESMTPSA id lj17-20020a170906f9d100b00888161349e0sm390679ejb.183.2023.01.29.05.12.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 29 Jan 2023 05:12:43 -0800 (PST) From: Efraim Flashner Date: Sun, 29 Jan 2023 15:12:35 +0200 Message-Id: <29b7080a94dbfdc13c890742a4fabcf1d731617c.1674997469.git.efraim@flashner.co.il> X-Mailer: git-send-email 2.39.1 In-Reply-To: References: 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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 From patchwork Sun Jan 29 13:12:36 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Efraim Flashner X-Patchwork-Id: 46514 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 6D16427BBED; Sun, 29 Jan 2023 13:13:23 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS 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 BEB5027BBE9 for ; Sun, 29 Jan 2023 13:13:21 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pM7UY-00037Z-2n; Sun, 29 Jan 2023 08:13:06 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pM7UW-00036i-6d for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pM7UV-0007jk-E1 for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pM7UV-0003Zx-9U for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61148] [PATCH 3/5] gnu: Add wfa2-lib. Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 29 Jan 2023 13:13:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61148 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61148@debbugs.gnu.org Cc: Efraim Flashner Received: via spool by 61148-submit@debbugs.gnu.org id=B61148.167499797613719 (code B ref 61148); Sun, 29 Jan 2023 13:13:03 +0000 Received: (at 61148) by debbugs.gnu.org; 29 Jan 2023 13:12:56 +0000 Received: from localhost ([127.0.0.1]:42430 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UN-0003Z4-JE for submit@debbugs.gnu.org; Sun, 29 Jan 2023 08:12:56 -0500 Received: from mail-ej1-f53.google.com ([209.85.218.53]:37433) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UJ-0003YL-E7 for 61148@debbugs.gnu.org; Sun, 29 Jan 2023 08:12:51 -0500 Received: by mail-ej1-f53.google.com with SMTP id ud5so24963047ejc.4 for <61148@debbugs.gnu.org>; Sun, 29 Jan 2023 05:12:51 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:from:to:cc:subject:date :message-id:reply-to; bh=YRttZ6A5URWe3rBjK6Cn62i95sXtm4invTeLsi0bA54=; b=AltrImexeI4CTT1qfE0q4Zaj5DjrpNOcy8ZU+9ovteOpa5hPmyxFgqGhpUOjQQ/mni oVnc+qadJ0vjUo0D8c0mJuwxyITOa+C5K5MkEpGAXrK5z2gw72KIjz7ouUKGFT93VZ0O 5q+b+Qkge2ELkRlvyja88J65os5D3iA/frhAjN+Rl1Pp30fk+ObCJQ//LeOSg6UvWwIz Gzm/gKCKtjHQmS6aZS3lP++k9I5Rx2HZ1NiWp3CJxAY9DQAcEoewM5nXp3gNbKqz22Wr cGNsa/VJjTvnaZHgLRJlv3fRAgPB+5u275bQ3i2I4OXGxTe4LYLUTk8cvVGHPtcOepdh bvCg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:x-gm-message-state:from :to:cc:subject:date:message-id:reply-to; bh=YRttZ6A5URWe3rBjK6Cn62i95sXtm4invTeLsi0bA54=; b=VZOMEGDtghi5G5PEkQ19mQdN6nyqIlSXoQDRj/2FtU7TtmLsCdeC/sPb+q+7IFK17J 6hvsIfi3nAOldw1MZ8YT1VzJayf9ZHBfdu8QwE/2nrMu6F068IcGj3df3iJTvhGKIbmm KnrTOWXySniTbXpd/tfvcfKviVGkALcxbCUjpxgWWdfnwT8J4QtSj5Xs5qAF8N4h4kQO Eww3s02aV17WS2vxF2AcwmSzlFlCEF93prNk6++gAcUk2b2uc37QOl+HC1nd1cpHbj6/ Mw6UgzG5/3i+F30ENMaKA3tI8HY21+DFbYJKzoCPiO42DoNZkH/K+vFk9sJAcLHJVuQM dNmQ== X-Gm-Message-State: AO0yUKUI9eeovM0XOlL6JTWm5z2liPyjfQImoRZ2fQQRjlZsNVyLRZWg rRsUk0R4aGedRuY/DilYLnzSfJbVBSSCVQ== X-Google-Smtp-Source: AK7set9t6eQy1wp/yJxrkLY9cz1isT2TfI3U4/NETgRN/4KqcRO3BycO1YiPxSwqxSL+wxXLO5TlKw== X-Received: by 2002:a17:906:d8c4:b0:87f:546d:7cb5 with SMTP id re4-20020a170906d8c400b0087f546d7cb5mr7051789ejb.37.1674997965842; Sun, 29 Jan 2023 05:12:45 -0800 (PST) Received: from localhost ([141.226.15.115]) by smtp.gmail.com with ESMTPSA id p2-20020a1709060e8200b008786675d086sm5224765ejf.29.2023.01.29.05.12.45 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 29 Jan 2023 05:12:45 -0800 (PST) From: Efraim Flashner Date: Sun, 29 Jan 2023 15:12:36 +0200 Message-Id: <8cd6e9d8b601af9fd507a60dd8efbd0b255eba96.1674997469.git.efraim@flashner.co.il> X-Mailer: git-send-email 2.39.1 In-Reply-To: References: 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (wfa2-lib): New variable. --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa0a6c0dd6..7b5d5c5e8c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15710,6 +15710,40 @@ (define-public tabixpp some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) +(define-public wfa2-lib + (let ((commit "188b522ae634add3c692ca7547595b7266f1fa19") + (revision "1")) + (package + (name "wfa2-lib") + (version (git-version "2.3.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smarco/WFA2-lib") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1pq844zsl7v5zk6pzkbh5j2k2g1ac54nlvgyihla2wlwi0ibndax")))) + (build-system cmake-build-system) + (arguments + (list + #:configure-flags + #~(list "-DOPENMP=ON"))) + (native-inputs + (list pkg-config)) + (home-page "https://github.com/ekg/tabixpp") + (synopsis "Wavefront alignment algorithm library") + (description "The @acronym{wavefront alignment, WFA} algorithm is an exact +gap-affine algorithm that takes advantage of homologous regions between the +sequences to accelerate the alignment process. Unlike to traditional dynamic +programming algorithms that run in quadratic time, the WFA runs in time +@code{O(ns+s^2)}, proportional to the sequence length @code{n} and the alignment +score @code{s}, using @code{O(s^2)} memory (or @code{O(s)} using the +ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple computational +patterns that the modern compilers can automatically vectorize for different +architectures without adapting the code.") + (license license:expat)))) + (define-public smithwaterman (let ((commit "2610e259611ae4cde8f03c72499d28f03f6d38a7")) (package From patchwork Sun Jan 29 13:12:37 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Efraim Flashner X-Patchwork-Id: 46515 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 2104327BBE9; Sun, 29 Jan 2023 13:13:25 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS autolearn=ham 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 B0AF527BBEB for ; Sun, 29 Jan 2023 13:13:22 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pM7UX-00037O-Qx; Sun, 29 Jan 2023 08:13:05 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pM7UW-000371-5Y for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pM7UV-0007l9-TJ for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pM7UV-0003a5-Nw for guix-patches@gnu.org; Sun, 29 Jan 2023 08:13:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61148] [PATCH 4/5] gnu: Add libvcfh. Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 29 Jan 2023 13:13:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61148 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61148@debbugs.gnu.org Cc: Efraim Flashner Received: via spool by 61148-submit@debbugs.gnu.org id=B61148.167499797613729 (code B ref 61148); Sun, 29 Jan 2023 13:13:03 +0000 Received: (at 61148) by debbugs.gnu.org; 29 Jan 2023 13:12:56 +0000 Received: from localhost ([127.0.0.1]:42432 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UO-0003ZD-7F for submit@debbugs.gnu.org; Sun, 29 Jan 2023 08:12:56 -0500 Received: from mail-ej1-f52.google.com ([209.85.218.52]:46854) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UL-0003YO-Ee for 61148@debbugs.gnu.org; Sun, 29 Jan 2023 08:12:53 -0500 Received: by mail-ej1-f52.google.com with SMTP id p26so13718091ejx.13 for <61148@debbugs.gnu.org>; Sun, 29 Jan 2023 05:12:53 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:from:to:cc:subject:date :message-id:reply-to; bh=dErTZnoju/vml+vpg9fT3B03qn4kYx3UtyCFlIYd62c=; b=iTnrX8noQnP++aWOd4pGucNovFSutSh1FOn6lNXuqB6foMVVKQNr726Wbl+xYn/TLn QQOvyXxmCPxViuYoJb0s8dOGovDUghvYrQxECIXOz3Ab5WItBEnDqpACeC+0D/2RsYCb LYkB6Zp9QzZkDWE5Md5hDa5u3Na2T5SPNg12ASdDEQZWS+V4F8rS6pvEyAlN4NNp+QX0 XlVl2HIM2e2XMD2wCeJKJiu8T/bI7Ox7ZoMh76zgDxDbk1AkWzNosBVy6ThZ0atjO5x6 Bti1JYy+ZCi5qoAFaIJ+fKrIZmL66dARxzrrxu7Z0nG+Nwth9FFl5yn5ioHn9hT+eAMc 39EQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:x-gm-message-state:from :to:cc:subject:date:message-id:reply-to; bh=dErTZnoju/vml+vpg9fT3B03qn4kYx3UtyCFlIYd62c=; b=W5x7t7/dJNipKaZw0OFGpe/+j4uEMhdR4lJ/tuGU2A8/wga2XCE2Mtxi6FwedPKGJX xTLD/sm1t5nYIJCzrsqlEzj3PdM0JHGqpDAueAeBqbcDbDVkzzBx4YQBUJNxTX3cT2lz Al+Cds2+3YYm7TJrU598iUD54GnmUwhhUeg4hXBEnOwovKywbF6q491W6e/8U3t9ddlJ AU/nRlXDJ5CFby4g1FGa2B2VQzifav0n/Y9w1b970ioYgkH82zQKVTDnvJvF0KT9BQVE 4d72yzyIVducNijiNqJ5GkpVSPrZgwINQWSEkVGAt5woLstgCee6/K7Dl1MwikOnRqIa 8Opg== X-Gm-Message-State: AFqh2kqK5/pKOCFM7xFJNc6Bkn5zAsmmTS8lJvATLyGiUvYRYhYqxNl9 SOj3jWLPXXMnyeGpBo3eRryg6cWncRQ+Hw== X-Google-Smtp-Source: AMrXdXvkb28eEBxZRIT/9v0zqfNCm6/VOm80JJQgzGbFy2g8E4Sml7vvkBCuQVWWj+tAwDbY73n+zw== X-Received: by 2002:a17:907:9b06:b0:872:f259:a7ea with SMTP id kn6-20020a1709079b0600b00872f259a7eamr48964691ejc.53.1674997967912; Sun, 29 Jan 2023 05:12:47 -0800 (PST) Received: from localhost ([141.226.15.115]) by smtp.gmail.com with ESMTPSA id p7-20020a170906b20700b0088478517830sm1758219ejz.83.2023.01.29.05.12.47 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 29 Jan 2023 05:12:47 -0800 (PST) From: Efraim Flashner Date: Sun, 29 Jan 2023 15:12:37 +0200 Message-Id: <9625ac451fe44ad7e2ea707e999cdc94d1389fce.1674997469.git.efraim@flashner.co.il> X-Mailer: git-send-email 2.39.1 In-Reply-To: References: 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (libvcfh): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7b5d5c5e8c..05a07af7f3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15744,6 +15744,43 @@ (define-public wfa2-lib architectures without adapting the code.") (license license:expat)))) +(define-public libvcfh + (let ((commit "44b6580639a216a484fd96de75a839091f25768a") + (revision "1")) + (package + (name "libvcfh") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/edawson/libVCFH.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jjqnzvai0849czh1hi5inm6y0228cw2s97i76f3vhyxj21mzvwm")))) + (build-system gnu-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; No configure script + (replace 'check + (lambda* (#:key tests? make-flags #:allow-other-keys) + (when tests? + (apply invoke "make" "test" make-flags) + (invoke "./test")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "libvcfh.a" (string-append out "/lib")) + (install-file "vcfheader.hpp" + (string-append out "/include/libvcfh")))))))) + (home-page "https://github.com/edawson/libVCFH") + (synopsis "Library for generating VCF headers") + (description "@code{libVCFH} is a set of data structures you can populate +to print a VCf header. It should be in spec with VCF4.1/4.2.") + (license license:expat)))) + (define-public smithwaterman (let ((commit "2610e259611ae4cde8f03c72499d28f03f6d38a7")) (package From patchwork Sun Jan 29 13:12:38 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Efraim Flashner X-Patchwork-Id: 46517 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 04BFE27BBED; Sun, 29 Jan 2023 13:14:10 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=ham 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 BD6CE27BBE9 for ; Sun, 29 Jan 2023 13:14:05 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pM7VU-0003Rf-D8; Sun, 29 Jan 2023 08:14:04 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pM7VT-0003Pz-20 for guix-patches@gnu.org; Sun, 29 Jan 2023 08:14:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pM7VS-0007qT-Hq for guix-patches@gnu.org; Sun, 29 Jan 2023 08:14:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pM7VS-0003cE-5n for guix-patches@gnu.org; Sun, 29 Jan 2023 08:14:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61148] [PATCH 5/5] gnu: vcflib: Update to 1.0.6. Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 29 Jan 2023 13:14:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61148 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61148@debbugs.gnu.org Cc: Efraim Flashner Received: via spool by 61148-submit@debbugs.gnu.org id=B61148.167499798713795 (code B ref 61148); Sun, 29 Jan 2023 13:14:02 +0000 Received: (at 61148) by debbugs.gnu.org; 29 Jan 2023 13:13:07 +0000 Received: from localhost ([127.0.0.1]:42438 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UY-0003aQ-Rv for submit@debbugs.gnu.org; Sun, 29 Jan 2023 08:13:07 -0500 Received: from mail-ej1-f53.google.com ([209.85.218.53]:44792) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UN-0003YV-82 for 61148@debbugs.gnu.org; Sun, 29 Jan 2023 08:12:56 -0500 Received: by mail-ej1-f53.google.com with SMTP id hx15so5399801ejc.11 for <61148@debbugs.gnu.org>; Sun, 29 Jan 2023 05:12:55 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:from:to:cc:subject:date :message-id:reply-to; bh=IY4uSkmft8vSQWEMcjXP/Wradrx5sfC818K9qWgQm54=; b=LuprAeUPFlzBVwh+eAkcPYdkmSHs/3yD4K6IEx4nLHa/BBRbNQdUBC1icL49HSNcSJ eQr4UshNFC/ddkZPvNhvPZaEHrNWVYxagAbYmJgIvysMA87EVF4cWpYzaCDWo/rdQOIJ InHjssLrko10PAXS3pBFYxlJOetegsAeeNKUnjYwa5q/j9XyK4v5SAZA+oL79H5XoJB8 nvWubiwj2uxWej6wRa0Ehqnhco2RCPPQ3grTMPBX0d8BuwJ+Wmdtwwg2IiEx+Tn8dp3T mBhL5vlukGnbxBTJV5VozLeP6ZEbW5FRpvwP853K1kvbSn2IjqVbgQkwPIaE6D7E7+hY 7RnQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:x-gm-message-state:from :to:cc:subject:date:message-id:reply-to; bh=IY4uSkmft8vSQWEMcjXP/Wradrx5sfC818K9qWgQm54=; b=R08/IQMtt34KPWKwYe5H/z3dPiVg89u5uo+VK57pJfU7KxzTysz6U1MQRw6sQa+vul mrp+bX/0mM0la33IZekT9Ub/FhsH9RQPyoGxva7upa1S4CyX6+KWiIc0r20Yt7nZRjpM QvvaaLVAqKP+NGD7P5stnkAP9+8/1SMugDgHzvMOkSniwpuPMoPesawIMa6lq4H+upTO TvKJ3MiLutxKOYN43TOyBRnMibR15yIEGQPkeL/hjgcJhbVuhmdfbBd+Q2+AuxYk63Zb r9PkPwH2QQMI5RSTG9ErLiiVpsR7kMMiKdWND2xFcdZ3f+FpZqWBjixxRZ4Sj3K2b64m Gs+Q== X-Gm-Message-State: AFqh2kpIp33k0ck+5QR0X3cIxBKCNpC5cSOhU36MpyO39Gn26+dcCOP4 aBxA/n5fmA9sNT5Fyf02uNhoCWkuQW4I5A== X-Google-Smtp-Source: AMrXdXvSiygmDHOfgsdpF8Tvxx60Uxmwl8oKQ/9jGmO92m69eeZ8TV6mzP9Q05gi3V33xflUjwoj8A== X-Received: by 2002:a17:906:644f:b0:877:6549:bb6 with SMTP id l15-20020a170906644f00b0087765490bb6mr39735353ejn.58.1674997969763; Sun, 29 Jan 2023 05:12:49 -0800 (PST) Received: from localhost ([141.226.15.115]) by smtp.gmail.com with ESMTPSA id m16-20020a1709062b9000b0084d4b8f5889sm5297048ejg.102.2023.01.29.05.12.49 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 29 Jan 2023 05:12:49 -0800 (PST) From: Efraim Flashner Date: Sun, 29 Jan 2023 15:12:38 +0200 Message-Id: X-Mailer: git-send-email 2.39.1 In-Reply-To: References: 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.6. [source]: Adjust snippet to use unbundled wfa2-lib include directory. Also unbundle simde, wfa2-lib. Remove googletest from unbundle list, it is no longer in use. [inputs]: Add curl, simde, wfa2-lib. [native-inputs]: Add pybind11, pandoc when available. Add the sources for libvcfh. [arguments]: Adjust configure-flags to build without zig and to use the unbundled wfa2-lib. Adjust custom 'build-shared-library phase for changes in the source. Adjust custom 'unpack-submodule-sources for changes in the source. --- gnu/packages/bioinformatics.scm | 69 +++++++++++++++++++++++++-------- 1 file changed, 52 insertions(+), 17 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 05a07af7f3..c4eeb6d68f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16033,74 +16033,108 @@ (define-public fastahack (define-public vcflib (package (name "vcflib") - (version "1.0.3") + (version "1.0.6") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/vcflib/vcflib") - (commit (string-append "v" version)))) + (commit (string-append "v" version)) + (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh")) + (base32 "0zcs8j3vdajram53srvjmq353f3prqdbn8fvzja4412w4zay79fz")) (modules '((guix build utils))) (snippet #~(begin (substitute* "CMakeLists.txt" ((".*fastahack.*") "") ((".*smithwaterman.*") "") + ;; Also look for fastahack and smithwaterman since + ;; we've just unbundled them. (("(pkg_check_modules\\(TABIXPP)" text) (string-append "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n" "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n" text)) + ;; Also link vcflib to fastahack and smithwaterman. (("\\$\\{TABIXPP_LIBRARIES\\}" text) (string-append "${FASTAHACK_LIBRARIES} " "${SMITHWATERMAN_LIBRARIES} " - text))) + text)) + ;; Honor setting WFA_INCLUDE_DIRS and not look at + ;; PREFIX/include/wfa2lib. + (((string-append "\\$\\{CMAKE_INSTALL_PREFIX\\}/" + "\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}/wfa2lib")) + "${WFA_INCLUDE_DIRS}")) (substitute* (find-files "." "\\.(h|c)(pp)?$") (("\"SmithWatermanGotoh.h\"") "") (("\"convert.h\"") "") (("\"disorder.h\"") "") (("Fasta.h") "fastahack/Fasta.h")) - (for-each delete-file-recursively - '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" - "libVCFH" "multichoose" "smithwaterman")))))) + (substitute* "src/Variant.h" + (("wavefront/wfa.hpp") "wfa2lib/wavefront/wfa.hpp")) + (delete-file-recursively "src/simde") + (with-directory-excursion "contrib" + (for-each delete-file-recursively + '(;"c-progress-bar" + "fastahack" + "filevercmp" + "fsom" + "intervaltree" + "libVCFH" + "multichoose" + "smithwaterman" + "tabixpp" + "WFA2-lib"))))))) (build-system cmake-build-system) (inputs (list bzip2 + curl htslib fastahack perl python + simde smithwaterman tabixpp + wfa2-lib xz zlib)) (native-inputs `(("pkg-config" ,pkg-config) + ("pybind11" ,pybind11) + ,@(if (member (%current-system) + (package-transitive-supported-systems pandoc)) + `(("pandoc" ,pandoc)) + '()) ;; Submodules. - ;; This package builds against the .o files so we need to extract the source. + ;; Not all of these packages provide libraries to link against. ("filevercmp-src" ,(package-source filevercmp)) ("fsom-src" ,(package-source fsom)) ("intervaltree-src" ,(package-source intervaltree)) + ("libvcfh-src" ,(package-source libvcfh)) ("multichoose-src" ,(package-source multichoose)))) (arguments (list #:configure-flags - #~(list (string-append + #~(list "-DZIG=NO" + "-DWFA_GITMODULE=OFF" + (string-append "-DWFA_INCLUDE_DIRS=" + (search-input-directory %build-inputs + "include/wfa2lib")) + "-DTABIX_FOUND=ON" ; Default to found + (string-append "-DPKG_CONFIG_EXECUTABLE=" (search-input-file %build-inputs (string-append "/bin/" #$(pkg-config-for-target))))) - #:tests? #f ; no tests + #:tests? #f ; Tests need more configuring. #: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")))) + (("vcflib STATIC") "vcflib SHARED")))) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs native-inputs #:allow-other-keys) (let ((unpack (lambda (source target) @@ -16114,10 +16148,11 @@ (define-public vcflib source "--strip-components=1"))))))) (and - (unpack "filevercmp-src" "filevercmp") - (unpack "fsom-src" "fsom") - (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose"))))) + (unpack "filevercmp-src" "contrib/filevercmp") + (unpack "fsom-src" "contrib/fsom") + (unpack "intervaltree-src" "contrib/intervaltree") + (unpack "libvcfh-src" "contrib/libvcfh") + (unpack "multichoose-src" "contrib/multichoose"))))) ;; This pkg-config file is provided by other distributions. (add-after 'install 'install-pkg-config-file (lambda* (#:key outputs #:allow-other-keys)