From unknown Mon Jun 23 13:14:25 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#61148] [PATCH 0/5] Update vcflib Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 29 Jan 2023 13:10:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61148 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61148@debbugs.gnu.org Cc: Pjotr Prins , Efraim Flashner X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.167499777713296 (code B ref -1); Sun, 29 Jan 2023 13:10:01 +0000 Received: (at submit) by debbugs.gnu.org; 29 Jan 2023 13:09:37 +0000 Received: from localhost ([127.0.0.1]:42417 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7R8-0003SG-KO for submit@debbugs.gnu.org; Sun, 29 Jan 2023 08:09:37 -0500 Received: from lists.gnu.org ([209.51.188.17]:53948) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7R6-0003S3-BM for submit@debbugs.gnu.org; Sun, 29 Jan 2023 08:09:32 -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 1pM7R6-0002Ma-5G for guix-patches@gnu.org; Sun, 29 Jan 2023 08:09:32 -0500 Received: from mail-ej1-x634.google.com ([2a00:1450:4864:20::634]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pM7R3-0006oU-Tw for guix-patches@gnu.org; Sun, 29 Jan 2023 08:09:31 -0500 Received: by mail-ej1-x634.google.com with SMTP id dr8so3349199ejc.12 for ; Sun, 29 Jan 2023 05:09:29 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:sender:from:to:cc:subject:date:message-id:reply-to; bh=TXvxgrGTBBxgtZrxCsayn1JLTKzVv5mVcGElui3wOzU=; b=T1biibWES8iLpe9ra8WaQHBknsHcdORRQQnONkAtCtCqUifurc8BSUujoJrDLCPlCV jZNkn/A5NNgF77u7sWNVC/JArDe+om36PPosAbeNJ3v5G/YjODiGMTkKLKCeX0uZvD0q jye97ATMF/OZywDqiutLLn9MkHsoFpOeWNBMnqECglk4P+jGBSMFIbmQ330BwZgcwOZJ u3APb/DF96FaiBFIk5kv25uQ4FUPJPO3h7HxlxqTbQI82Z3n/N/ZLC+l82QzqT/hWwgF YX051dlDrADcPCfANqDFgN9T3qTLzt2dDYNxOMxqAjdxJmfKt2LVbvYDN/z8XOZ16g7X FlXg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:sender:x-gm-message-state:from:to:cc:subject:date :message-id:reply-to; bh=TXvxgrGTBBxgtZrxCsayn1JLTKzVv5mVcGElui3wOzU=; b=cGOpBCJKJvhovIbmGfxBrnITT9ziSldMRdFKjDFOMpT1g2FfLEPLnMM/eLULNyT0lR tJPDnTgO5DCupl/3foBVQlLSSFSH/LaplrSrE4VYy0TgvHEU0le9n5GLwdmeu/UczAlu gg/22wBKglo0+teZgkO+e2z4Xz/fAd9ojnkG1ORoGunXdiA6mIyFuiuD1xbDC9PLEhLc UOyF5zY/jVM0zfwUV/6uuwMfQxrj7Eykuf2s15cBYe2dSrWLaMTCmk5h1XLoGge9VXgQ yC5HVzcJ4pdeXjnYzw5qBmIMcn9Q6kXLOTT4LGtwRome9qsjj3WNDSdflMgmnyIqzeVa MjuA== X-Gm-Message-State: AO0yUKWETG+ir6faxKRCsmcUIaelTL/nf0mothdfjnjpb1qXFDbsuloB NKQw+z+udpA859g1zQYxprDWWIYkADACzA== X-Google-Smtp-Source: AK7set92Ywcbh9WhG3aVztBRCWaM78EddwyT42BaS/S4767G+eUc3DPUYyl0otMzC+sFW0sw5/e8Rw== X-Received: by 2002:a17:906:cc8a:b0:878:72d0:2817 with SMTP id oq10-20020a170906cc8a00b0087872d02817mr12367121ejb.29.1674997767344; Sun, 29 Jan 2023 05:09:27 -0800 (PST) Received: from localhost ([141.226.15.115]) by smtp.gmail.com with ESMTPSA id bh13-20020a170906a0cd00b0084d14646fd9sm5230458ejb.165.2023.01.29.05.09.26 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 29 Jan 2023 05:09:26 -0800 (PST) From: Efraim Flashner Date: Sun, 29 Jan 2023 15:09:24 +0200 Message-Id: X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::634; envelope-from=efraim.flashner@gmail.com; helo=mail-ej1-x634.google.com X-Spam_score_int: -14 X-Spam_score: -1.5 X-Spam_bar: - X-Spam_report: (-1.5 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FORGED_FROMDOMAIN=0.249, FREEMAIL_FROM=0.001, HEADER_FROM_DIFFERENT_DOMAINS=0.249, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.1 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.1 (--) vcflib has a new update out so it's time to update it and the dependant packages. libvcfh doesn't seem to be used, perhaps Pjotr knows if it's needed? I don't love '-DTABIX_FOUND=ON' in vcflib but it seems to work. I'm also not sure that the simde headers are actually used. I'd like to use more of the unbundled sources since it seems like a waste to unbundle them and then just toss the sources back into the build but they don't natively produce libraries so I'd rather not. Perhaps it'd be better to just not unbundle them in the first place? Efraim Flashner (5): gnu: intervaltree: Update to 0.1-1.aa59377. gnu: tabixpp: Update to 1.1.2. gnu: Add wfa2-lib. gnu: Add libvcfh. gnu: vcflib: Update to 1.0.6. gnu/packages/bioinformatics.scm | 217 ++++++++++++++++++++++++-------- 1 file changed, 166 insertions(+), 51 deletions(-) base-commit: b9e6e31877cdb96cceba4d1ec6268f86b824dec4 -- 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 From unknown Mon Jun 23 13:14:25 2025 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 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.3 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.7 (/) * 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 -- 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 From unknown Mon Jun 23 13:14:25 2025 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 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.3 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.7 (/) * 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 From unknown Mon Jun 23 13:14:25 2025 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 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.3 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.7 (/) * 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 -- 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 From unknown Mon Jun 23 13:14:25 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#61148] [PATCH 4/5] gnu: Add libvcfh. 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(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 -- 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 From unknown Mon Jun 23 13:14:25 2025 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 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.3 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.7 (/) * 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) -- 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 From unknown Mon Jun 23 13:14:25 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#61148] [PATCH 0/5] Update vcflib References: In-Reply-To: Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 27 Oct 2023 12:41:02 +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 Received: via spool by 61148-submit@debbugs.gnu.org id=B61148.169841043511063 (code B ref 61148); Fri, 27 Oct 2023 12:41:02 +0000 Received: (at 61148) by debbugs.gnu.org; 27 Oct 2023 12:40:35 +0000 Received: from localhost ([127.0.0.1]:35316 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qwM8h-0002sM-BL for submit@debbugs.gnu.org; Fri, 27 Oct 2023 08:40:35 -0400 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21726) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qwM8c-0002s4-5N for 61148@debbugs.gnu.org; Fri, 27 Oct 2023 08:40:33 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1698410396; cv=none; d=zohomail.com; s=zohoarc; b=k6H7fQk6xRhmu59TtjUKGy6qB0t6v+7v1ovRKfis2ibmZwGn96rMtfe2fZtvsMnf37YXmDxhFh7L7zB3ViNaNYoBi1qTYJUCvPgotTPC24wbkMg4+8uLcze8XeRwon8fCASx2Yz6wY44kwTHrDMqP2QXheAHbB6GiUGPRShhFxM= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1698410396; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=Ad9AZB1R/1+5Fo9b8TRki2CgXhJ0c8GeRtfkt6y/p8k=; b=Mm8lEbNW/VhFu8JwsZz5y4EMe5atbAdAwm+RCDarpRIRM1cIKRzasxPSxLqBt9CfNE0SFf6YqzNj+AxxEgPmHRy5tzxvJra9t7S9B2qoflGMZYj0bcGsTUFipAEXf9u5kiVH6kcQIgBBFHqYSriKFcoq5QRdT1JjrH0DZXZMSGM= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1698410396; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=Ad9AZB1R/1+5Fo9b8TRki2CgXhJ0c8GeRtfkt6y/p8k=; b=NoaD9KiEw6jV5U7yMLt7cwIunVUkAcjtLslyYR+sYWebsPz4srBdTuMkNPjjYIo7 zmDQUZ6CaNc3HFOg2hxTP8eC8qeQ7UUacZzdKD0VfgL0lwemgt2HSFhacP/21Z2Cu39 2QOlekOoZoAIkhn0W6dF1ZwRKMnjmPm1PVf7AA8o= Received: from localhost (141.80.246.165 [141.80.246.165]) by mx.zohomail.com with SMTPS id 1698410395890488.7923392482079; Fri, 27 Oct 2023 05:39:55 -0700 (PDT) User-agent: mu4e 1.10.7; emacs 29.1 From: Ricardo Wurmus Date: Fri, 27 Oct 2023 14:38:53 +0200 Message-ID: <874jici6hy.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) These patches look good to me. One note: you can use #$output directly instead of (assoc-ref outputs "out"). -- Ricardo From unknown Mon Jun 23 13:14:25 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Efraim Flashner Subject: bug#61148: closed (Re: [PATCH 0/5] Update vcflib) Message-ID: References: <87iko6kspm.fsf@nicolasgoaziou.fr> X-Gnu-PR-Message: they-closed 61148 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 61148@debbugs.gnu.org Date: Tue, 18 Mar 2025 20:09:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1742328542-20372-1" This is a multi-part message in MIME format... ------------=_1742328542-20372-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #61148: [PATCH 0/5] Update vcflib which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 61148@debbugs.gnu.org. --=20 61148: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D61148 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1742328542-20372-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 61148-done) by debbugs.gnu.org; 18 Mar 2025 20:08:33 +0000 Received: from localhost ([127.0.0.1]:43406 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tudEm-0005Dz-PK for submit@debbugs.gnu.org; Tue, 18 Mar 2025 16:08:33 -0400 Received: from msg-3.mailo.com ([213.182.54.8]:36636 helo=mailo.com) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tudEi-0005CV-QA for 61148-done@debbugs.gnu.org; Tue, 18 Mar 2025 16:08:30 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=simple/simple; d=nicolasgoaziou.fr; s=mailo; t=1742328501; bh=e7LrG1yBMYyTFE3KwX3u25GkdmUtGdn7cgqLDER8Wu4=; h=X-EA-Auth:From:To:Subject:In-Reply-To:Date:Message-ID: MIME-Version:Content-Type; b=New/fpz7cRbcZc60EH/sCHEEpEXxOwZThJ7RJ5aE6+d33mmmTZchLLjqz6aXOVNOu hwKI2R2p++CcE/Uq6IzgcxaJ/zBKJHsox9zS66vmVwuNuBcHhAJJbWDpzYWhGkpw0H jnMUZOQsEIi8leDS44aGeTaGlD4P93nIGIltbK80= Received: by b221-9.in.mailobj.net [192.168.90.29] with ESMTP via ip-20.mailobj.net [213.182.54.20] Tue, 18 Mar 2025 21:08:21 +0100 (CET) X-EA-Auth: iqtieT6ngbRPLLmoPc1vNwwpVwqtf4AbDcE1mrgARWhAXCffYEqmepiDATfRMY2dgO/jfsEYTx+5RAJ74AeSUgE2ZbUckf9D1Xrw91w5Y/U= From: Nicolas Goaziou To: 61148-done@debbugs.gnu.org Subject: Re: [PATCH 0/5] Update vcflib In-Reply-To: <874jici6hy.fsf@elephly.net> Date: Tue, 18 Mar 2025 21:08:05 +0100 Message-ID: <87iko6kspm.fsf@nicolasgoaziou.fr> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 61148-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) vcflib is already at a higher version. Closing. ------------=_1742328542-20372-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 29 Jan 2023 13:09:37 +0000 Received: from localhost ([127.0.0.1]:42417 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7R8-0003SG-KO for submit@debbugs.gnu.org; Sun, 29 Jan 2023 08:09:37 -0500 Received: from lists.gnu.org ([209.51.188.17]:53948) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7R6-0003S3-BM for submit@debbugs.gnu.org; Sun, 29 Jan 2023 08:09:32 -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 1pM7R6-0002Ma-5G for guix-patches@gnu.org; Sun, 29 Jan 2023 08:09:32 -0500 Received: from mail-ej1-x634.google.com ([2a00:1450:4864:20::634]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pM7R3-0006oU-Tw for guix-patches@gnu.org; Sun, 29 Jan 2023 08:09:31 -0500 Received: by mail-ej1-x634.google.com with SMTP id dr8so3349199ejc.12 for ; Sun, 29 Jan 2023 05:09:29 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:sender:from:to:cc:subject:date:message-id:reply-to; bh=TXvxgrGTBBxgtZrxCsayn1JLTKzVv5mVcGElui3wOzU=; b=T1biibWES8iLpe9ra8WaQHBknsHcdORRQQnONkAtCtCqUifurc8BSUujoJrDLCPlCV jZNkn/A5NNgF77u7sWNVC/JArDe+om36PPosAbeNJ3v5G/YjODiGMTkKLKCeX0uZvD0q jye97ATMF/OZywDqiutLLn9MkHsoFpOeWNBMnqECglk4P+jGBSMFIbmQ330BwZgcwOZJ u3APb/DF96FaiBFIk5kv25uQ4FUPJPO3h7HxlxqTbQI82Z3n/N/ZLC+l82QzqT/hWwgF YX051dlDrADcPCfANqDFgN9T3qTLzt2dDYNxOMxqAjdxJmfKt2LVbvYDN/z8XOZ16g7X FlXg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:sender:x-gm-message-state:from:to:cc:subject:date :message-id:reply-to; bh=TXvxgrGTBBxgtZrxCsayn1JLTKzVv5mVcGElui3wOzU=; b=cGOpBCJKJvhovIbmGfxBrnITT9ziSldMRdFKjDFOMpT1g2FfLEPLnMM/eLULNyT0lR tJPDnTgO5DCupl/3foBVQlLSSFSH/LaplrSrE4VYy0TgvHEU0le9n5GLwdmeu/UczAlu gg/22wBKglo0+teZgkO+e2z4Xz/fAd9ojnkG1ORoGunXdiA6mIyFuiuD1xbDC9PLEhLc UOyF5zY/jVM0zfwUV/6uuwMfQxrj7Eykuf2s15cBYe2dSrWLaMTCmk5h1XLoGge9VXgQ yC5HVzcJ4pdeXjnYzw5qBmIMcn9Q6kXLOTT4LGtwRome9qsjj3WNDSdflMgmnyIqzeVa MjuA== X-Gm-Message-State: AO0yUKWETG+ir6faxKRCsmcUIaelTL/nf0mothdfjnjpb1qXFDbsuloB NKQw+z+udpA859g1zQYxprDWWIYkADACzA== X-Google-Smtp-Source: AK7set92Ywcbh9WhG3aVztBRCWaM78EddwyT42BaS/S4767G+eUc3DPUYyl0otMzC+sFW0sw5/e8Rw== X-Received: by 2002:a17:906:cc8a:b0:878:72d0:2817 with SMTP id oq10-20020a170906cc8a00b0087872d02817mr12367121ejb.29.1674997767344; Sun, 29 Jan 2023 05:09:27 -0800 (PST) Received: from localhost ([141.226.15.115]) by smtp.gmail.com with ESMTPSA id bh13-20020a170906a0cd00b0084d14646fd9sm5230458ejb.165.2023.01.29.05.09.26 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 29 Jan 2023 05:09:26 -0800 (PST) From: Efraim Flashner To: guix-patches@gnu.org Subject: [PATCH 0/5] Update vcflib Date: Sun, 29 Jan 2023 15:09:24 +0200 Message-Id: X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::634; envelope-from=efraim.flashner@gmail.com; helo=mail-ej1-x634.google.com X-Spam_score_int: -14 X-Spam_score: -1.5 X-Spam_bar: - X-Spam_report: (-1.5 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FORGED_FROMDOMAIN=0.249, FREEMAIL_FROM=0.001, HEADER_FROM_DIFFERENT_DOMAINS=0.249, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.1 (-) X-Debbugs-Envelope-To: submit Cc: Pjotr Prins , Efraim Flashner X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.1 (--) vcflib has a new update out so it's time to update it and the dependant packages. libvcfh doesn't seem to be used, perhaps Pjotr knows if it's needed? I don't love '-DTABIX_FOUND=ON' in vcflib but it seems to work. I'm also not sure that the simde headers are actually used. I'd like to use more of the unbundled sources since it seems like a waste to unbundle them and then just toss the sources back into the build but they don't natively produce libraries so I'd rather not. Perhaps it'd be better to just not unbundle them in the first place? Efraim Flashner (5): gnu: intervaltree: Update to 0.1-1.aa59377. gnu: tabixpp: Update to 1.1.2. gnu: Add wfa2-lib. gnu: Add libvcfh. gnu: vcflib: Update to 1.0.6. gnu/packages/bioinformatics.scm | 217 ++++++++++++++++++++++++-------- 1 file changed, 166 insertions(+), 51 deletions(-) base-commit: b9e6e31877cdb96cceba4d1ec6268f86b824dec4 -- 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 ------------=_1742328542-20372-1--