From patchwork Fri Apr 16 09:55:39 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Roel Janssen X-Patchwork-Id: 28585 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 0F86927BC82; Fri, 16 Apr 2021 10:56:12 +0100 (BST) 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,SPF_HELO_PASS,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 2214A27BC6C for ; Fri, 16 Apr 2021 10:56:11 +0100 (BST) Received: from localhost ([::1]:46962 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lXLCs-0006xB-9S for patchwork@mira.cbaines.net; Fri, 16 Apr 2021 05:56:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:49200) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lXLCk-0006wq-Ra for guix-patches@gnu.org; Fri, 16 Apr 2021 05:56:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:56753) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lXLCk-0003X6-Hb for guix-patches@gnu.org; Fri, 16 Apr 2021 05:56:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lXLCk-0008VM-GL for guix-patches@gnu.org; Fri, 16 Apr 2021 05:56:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 16 Apr 2021 09:56:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 47821 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47821@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.161856695032673 (code B ref -1); Fri, 16 Apr 2021 09:56:02 +0000 Received: (at submit) by debbugs.gnu.org; 16 Apr 2021 09:55:50 +0000 Received: from localhost ([127.0.0.1]:40066 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lXLCX-0008Uv-H9 for submit@debbugs.gnu.org; Fri, 16 Apr 2021 05:55:50 -0400 Received: from lists.gnu.org ([209.51.188.17]:48572) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lXLCT-0008Uh-9G for submit@debbugs.gnu.org; Fri, 16 Apr 2021 05:55:48 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:49192) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lXLCS-0006wW-W8 for guix-patches@gnu.org; Fri, 16 Apr 2021 05:55:45 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:57238) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lXLCS-0003L1-PN for guix-patches@gnu.org; Fri, 16 Apr 2021 05:55:44 -0400 Received: from 2001-1c02-0b18-2900-222e-248e-9586-e52d.cable.dynamic.v6.ziggo.nl ([2001:1c02:b18:2900:222e:248e:9586:e52d]:48092) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1lXLCP-0002sD-Tk for guix-patches@gnu.org; Fri, 16 Apr 2021 05:55:44 -0400 Message-ID: <9345d6a11fd99f1a8eefeb3664508938255e1287.camel@gnu.org> From: Roel Janssen Date: Fri, 16 Apr 2021 11:55:39 +0200 User-Agent: Evolution 3.38.4 (3.38.4-1.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 Hi Guix, The following patches update htslib, bcftools, samtools, and bedtools. I've succesfully built bedtools with the latest samtools instead of the 1.9 version. Kind regards, Roel Janssen From 45e578976cd0c77e60d2188385adcda51b23b92a Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Fri, 16 Apr 2021 11:49:49 +0200 Subject: [PATCH 1/4] gnu: htslib: Update to 1.12. * gnu/packages/bioinformatics.scm (htslib): Update to 1.12. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 41ef4cd513..e385e07cea 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4476,7 +4476,7 @@ performance.") (define-public htslib (package (name "htslib") - (version "1.11") + (version "1.12") (source (origin (method url-fetch) (uri (string-append @@ -4484,7 +4484,7 @@ performance.") version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng")))) + "1jplnvizgr0fyyvvmkfmnsywrrpqhid3760vw15bllz98qdi9012")))) (build-system gnu-build-system) ;; Let htslib translate "gs://" and "s3://" to regular https links with ;; "--enable-gcs" and "--enable-s3". For these options to work, we also -- 2.30.2