From patchwork Fri Nov 13 11:01:04 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Roel Janssen X-Patchwork-Id: 25109 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 9822327BBF6; Fri, 13 Nov 2020 11:02:14 +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,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 1002A27BBF4 for ; Fri, 13 Nov 2020 11:02:14 +0000 (GMT) Received: from localhost ([::1]:45196 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdWqL-0007J0-2n for patchwork@mira.cbaines.net; Fri, 13 Nov 2020 06:02:13 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:42908) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kdWqA-0007GT-2W for guix-patches@gnu.org; Fri, 13 Nov 2020 06:02:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:35322) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kdWq9-0003Yd-Nh for guix-patches@gnu.org; Fri, 13 Nov 2020 06:02:01 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kdWq9-0001Jk-Kl for guix-patches@gnu.org; Fri, 13 Nov 2020 06:02:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#44613] [PATCH] Fix build for bedtools Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 13 Nov 2020 11:02:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 44613 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 44613@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.16052652855014 (code B ref -1); Fri, 13 Nov 2020 11:02:01 +0000 Received: (at submit) by debbugs.gnu.org; 13 Nov 2020 11:01:25 +0000 Received: from localhost ([127.0.0.1]:46868 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdWpY-0001Io-P0 for submit@debbugs.gnu.org; Fri, 13 Nov 2020 06:01:25 -0500 Received: from lists.gnu.org ([209.51.188.17]:60528) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdWpX-0001Ig-1s for submit@debbugs.gnu.org; Fri, 13 Nov 2020 06:01:23 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:42704) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kdWpP-0006a6-Nz for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:19 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:48998) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdWpL-0003H1-IN for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:14 -0500 Received: from [143.121.239.14] (port=45168 helo=[10.132.152.6]) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kdWpG-0002NT-Ip for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:10 -0500 Message-ID: From: Roel Janssen Date: Fri, 13 Nov 2020 12:01:04 +0100 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 Dear Guix, By updating samtools to 1.11, I introduced a build failure for bedtools. More precisely, the tests for intersect break in precisely this way: https://github.com/arq5x/bedtools2/issues/814 With the following patches, I'd like to add samtools-1.9, htslib-1.9 (samtools depends on that) to fix this problem with bedtools. Alternatively we could add a patch to disable the failing bedtools tests. I manually inspected the test results, and seem to match perfectly (indicating that there's no problem with bedtools). Kind regards, Roel Janssen From 220604159383b09e11a7b0bed51237257c7c0442 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Fri, 13 Nov 2020 11:28:43 +0100 Subject: [PATCH 1/3] gnu: Add htslib-1.9. * gnu/packages/bioinformatics.scm (htslib-1.9): New variable. --- gnu/packages/bioinformatics.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 06972dee51..ba86333fc3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4250,6 +4250,19 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and ;; the rest is released under the Expat license (license (list license:expat license:bsd-3)))) +(define-public htslib-1.9 + (package (inherit htslib) + (name "htslib") + (version "1.9") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/samtools/htslib/releases/download/" + version "/htslib-" version ".tar.bz2")) + (sha256 + (base32 + "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0")))))) + ;; This package should be removed once no packages rely upon it. (define htslib-1.3 (package -- 2.29.2