From patchwork Thu Oct 29 11:01:07 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Roel Janssen X-Patchwork-Id: 24871 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 65DC327BBF3; Thu, 29 Oct 2020 11:02:18 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.9 required=5.0 tests=BAYES_00,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id E10CE27BBF2 for ; Thu, 29 Oct 2020 11:02:17 +0000 (GMT) Received: from localhost ([::1]:42256 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kY5hB-0002AA-2i for patchwork@mira.cbaines.net; Thu, 29 Oct 2020 07:02:17 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:51954) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kY5gw-00029r-PL for guix-patches@gnu.org; Thu, 29 Oct 2020 07:02:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40446) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kY5gw-00051B-Fr for guix-patches@gnu.org; Thu, 29 Oct 2020 07:02:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kY5gw-0004XJ-Ca for guix-patches@gnu.org; Thu, 29 Oct 2020 07:02:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#44304] [PATCH] gnu: Update htslib to 1.11. Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 29 Oct 2020 11:02:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 44304 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 44304@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org X-Debbugs-Original-Cc: 44304@debbugs.gnu.org Received: via spool by submit@debbugs.gnu.org id=B.160396928617372 (code B ref -1); Thu, 29 Oct 2020 11:02:02 +0000 Received: (at submit) by debbugs.gnu.org; 29 Oct 2020 11:01:26 +0000 Received: from localhost ([127.0.0.1]:51989 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kY5gM-0004W8-6L for submit@debbugs.gnu.org; Thu, 29 Oct 2020 07:01:26 -0400 Received: from lists.gnu.org ([209.51.188.17]:59258) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kY5gK-0004W0-QT for submit@debbugs.gnu.org; Thu, 29 Oct 2020 07:01:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:51898) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kY5gK-00027I-G3 for guix-patches@gnu.org; Thu, 29 Oct 2020 07:01:24 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:37878) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kY5gK-0004pz-5L; Thu, 29 Oct 2020 07:01:24 -0400 Received: from 2001-1c02-0b2a-aa00-93bf-7c8c-0fae-b738.cable.dynamic.v6.ziggo.nl ([2001:1c02:b2a:aa00:93bf:7c8c:fae:b738]:49470) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kY5g8-0000xs-N2; Thu, 29 Oct 2020 07:01:20 -0400 Message-ID: <08b421af5c82326cae13054e014e926b6b3c4ece.camel@gnu.org> From: Roel Janssen Date: Thu, 29 Oct 2020 12:01:07 +0100 In-Reply-To: <6ccd23fc29b49611b82d9cc26461dfc294796aa3.camel@gnu.org> References: <6ccd23fc29b49611b82d9cc26461dfc294796aa3.camel@gnu.org> User-Agent: Evolution 3.38.1 (3.38.1-1.fc33) MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches On Thu, 2020-10-29 at 11:44 +0100, Roel Janssen wrote: > Dear Guix, > > I'd like to update htslib to 1.11.  The patch is straightfoward. > > Kind regards, > Roel Janssen In addition to htslib, it'd be good to keep samtools and bcftools in sync. So here are the patches for bcftools and samtools. Kind regards, Roel Janssen From 20a16449cd640f32798cb36f942eb44faaa9f661 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 29 Oct 2020 11:57:16 +0100 Subject: [PATCH 2/3] gnu: Update bcftools to 1.11. * gnu/packages/bioinformatics.scm (bcftools): Update to 1.11. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 09216f6a8d..a428ba1fed 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -313,7 +313,7 @@ BAM files.") (define-public bcftools (package (name "bcftools") - (version "1.9") + (version "1.11") (source (origin (method url-fetch) (uri (string-append "https://github.com/samtools/bcftools/" @@ -321,11 +321,11 @@ BAM files.") version "/bcftools-" version ".tar.bz2")) (sha256 (base32 - "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg")) + "0r508mp15pqzf8r1269kb4v5naw9zsvbwd3cz8s1yj7carsf9viw")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.9") + (delete-file-recursively "htslib-1.11") #t)))) (build-system gnu-build-system) (arguments -- 2.26.2