From patchwork Tue Oct 6 08:48:31 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Roel Janssen X-Patchwork-Id: 24485 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 C771227BBE9; Tue, 6 Oct 2020 09:49:08 +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,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 9778A27BBE8 for ; Tue, 6 Oct 2020 09:49:08 +0100 (BST) Received: from localhost ([::1]:56404 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kPieh-0002Fc-Lz for patchwork@mira.cbaines.net; Tue, 06 Oct 2020 04:49:07 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56898) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kPiec-0002F3-4T for guix-patches@gnu.org; Tue, 06 Oct 2020 04:49:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40084) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kPieb-0003og-RR for guix-patches@gnu.org; Tue, 06 Oct 2020 04:49:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kPieb-0008GG-QZ for guix-patches@gnu.org; Tue, 06 Oct 2020 04:49:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#43825] [PATCH] bioinformatics: htslib: Enable support for custom URI schemes. Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 06 Oct 2020 08:49:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 43825 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 43825@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.160197412031723 (code B ref -1); Tue, 06 Oct 2020 08:49:01 +0000 Received: (at submit) by debbugs.gnu.org; 6 Oct 2020 08:48:40 +0000 Received: from localhost ([127.0.0.1]:51630 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kPieF-0008Fb-Mf for submit@debbugs.gnu.org; Tue, 06 Oct 2020 04:48:39 -0400 Received: from lists.gnu.org ([209.51.188.17]:44984) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kPieC-0008FS-Tl for submit@debbugs.gnu.org; Tue, 06 Oct 2020 04:48:37 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56866) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kPieC-00029y-MM for guix-patches@gnu.org; Tue, 06 Oct 2020 04:48:36 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:47824) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kPieC-0003nZ-E5 for guix-patches@gnu.org; Tue, 06 Oct 2020 04:48:36 -0400 Received: from 2001-1c02-0b2a-aa00-535e-258b-a1d8-1018.cable.dynamic.v6.ziggo.nl ([2001:1c02:b2a:aa00:535e:258b:a1d8:1018]:57072) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kPieA-0005b2-IS for guix-patches@gnu.org; Tue, 06 Oct 2020 04:48:35 -0400 Message-ID: From: Roel Janssen Date: Tue, 06 Oct 2020 10:48:31 +0200 User-Agent: Evolution 3.36.5 (3.36.5-1.fc32) 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, I'd like to apply this patch to enable accessing files stored in certain "cloud" systems. I added "--enable-libcurl" although it is not strictly necessary. Both "--enable-gcs" and "--enable-s3" require libcurl to be enabled, so this just seems reassuringly clear to me. Kind regards, Roel Janssen From fbec05df4bcc630ac51f59cd27f8e45a6ac41002 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 6 Oct 2020 10:41:56 +0200 Subject: [PATCH] bioinformatics: htslib: Enable support for custom URI schemes. This commit enables the translation of "gs://" and "s3://" URIs into their equivalent HTTPS variants. * gnu/packages/bioinformatics.scm (htslib): Enable support for custom URIs. --- gnu/packages/bioinformatics.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fda7255662..c8bf7cfdad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4225,6 +4225,10 @@ performance.") (base32 "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0")))) (build-system gnu-build-system) + (arguments + `(#:configure-flags '("--enable-gcs" + "--enable-libcurl" + "--enable-s3"))) (inputs `(("curl" ,curl) ("openssl" ,openssl))) -- 2.26.2