From unknown Mon Aug 18 00:08:12 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#43825 <43825@debbugs.gnu.org> To: bug#43825 <43825@debbugs.gnu.org> Subject: Status: [PATCH] bioinformatics: htslib: Enable support for custom URI schemes. Reply-To: bug#43825 <43825@debbugs.gnu.org> Date: Mon, 18 Aug 2025 07:08:12 +0000 retitle 43825 [PATCH] bioinformatics: htslib: Enable support for custom URI= schemes. reassign 43825 guix-patches submitter 43825 Roel Janssen severity 43825 normal tag 43825 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 06 04:48:40 2020 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: Subject: [PATCH] bioinformatics: htslib: Enable support for custom URI schemes. From: Roel Janssen To: guix-patches@gnu.org Date: Tue, 06 Oct 2020 10:48:31 +0200 Content-Type: multipart/mixed; boundary="=-kHJ4d/rTSsWBBELwW6pX" User-Agent: Evolution 3.36.5 (3.36.5-1.fc32) MIME-Version: 1.0 X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: submit 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: -3.3 (---) --=-kHJ4d/rTSsWBBELwW6pX Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit 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 --=-kHJ4d/rTSsWBBELwW6pX Content-Disposition: attachment; filename*0=0001-bioinformatics-htslib-Enable-support-for-custom-URI-.pat; filename*1=ch Content-Transfer-Encoding: base64 Content-Type: text/x-patch; name="0001-bioinformatics-htslib-Enable-support-for-custom-URI-.patch"; charset="UTF-8" RnJvbSBmYmVjMDVkZjRiY2M2MzBhYzUxZjU5Y2QyN2Y4ZTQ1YTZhYzQxMDAyIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiBSb2VsIEphbnNzZW4gPHJvZWxAZ251Lm9yZz4KRGF0ZTogVHVl LCA2IE9jdCAyMDIwIDEwOjQxOjU2ICswMjAwClN1YmplY3Q6IFtQQVRDSF0gYmlvaW5mb3JtYXRp Y3M6IGh0c2xpYjogRW5hYmxlIHN1cHBvcnQgZm9yIGN1c3RvbSBVUkkKIHNjaGVtZXMuCgpUaGlz IGNvbW1pdCBlbmFibGVzIHRoZSB0cmFuc2xhdGlvbiBvZiAiZ3M6Ly8iIGFuZCAiczM6Ly8iClVS SXMgaW50byB0aGVpciBlcXVpdmFsZW50IEhUVFBTIHZhcmlhbnRzLgoKKiBnbnUvcGFja2FnZXMv YmlvaW5mb3JtYXRpY3Muc2NtIChodHNsaWIpOiBFbmFibGUgc3VwcG9ydCBmb3IgY3VzdG9tIFVS SXMuCi0tLQogZ251L3BhY2thZ2VzL2Jpb2luZm9ybWF0aWNzLnNjbSB8IDQgKysrKwogMSBmaWxl IGNoYW5nZWQsIDQgaW5zZXJ0aW9ucygrKQoKZGlmZiAtLWdpdCBhL2dudS9wYWNrYWdlcy9iaW9p bmZvcm1hdGljcy5zY20gYi9nbnUvcGFja2FnZXMvYmlvaW5mb3JtYXRpY3Muc2NtCmluZGV4IGZk YTcyNTU2NjIuLmM4YmY3Y2ZkYWQgMTAwNjQ0Ci0tLSBhL2dudS9wYWNrYWdlcy9iaW9pbmZvcm1h dGljcy5zY20KKysrIGIvZ251L3BhY2thZ2VzL2Jpb2luZm9ybWF0aWNzLnNjbQpAQCAtNDIyNSw2 ICs0MjI1LDEwIEBAIHBlcmZvcm1hbmNlLiIpCiAgICAgICAgICAgICAgICAoYmFzZTMyCiAgICAg ICAgICAgICAgICAgIjE2bGp2NDNzYzNmeG12NjN3N2IyZmY4bTFzN2g4OXhoYXp3bWJtMWJpY3o4 YXhxOGZqejAiKSkpKQogICAgIChidWlsZC1zeXN0ZW0gZ251LWJ1aWxkLXN5c3RlbSkKKyAgICAo YXJndW1lbnRzCisgICAgIGAoIzpjb25maWd1cmUtZmxhZ3MgJygiLS1lbmFibGUtZ2NzIgorICAg ICAgICAgICAgICAgICAgICAgICAgICAgIi0tZW5hYmxlLWxpYmN1cmwiCisgICAgICAgICAgICAg ICAgICAgICAgICAgICAiLS1lbmFibGUtczMiKSkpCiAgICAgKGlucHV0cwogICAgICBgKCgiY3Vy bCIgLGN1cmwpCiAgICAgICAgKCJvcGVuc3NsIiAsb3BlbnNzbCkpKQotLSAKMi4yNi4yCgo= --=-kHJ4d/rTSsWBBELwW6pX-- From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 06 15:24:46 2020 Received: (at 43825) by debbugs.gnu.org; 6 Oct 2020 19:24:46 +0000 Received: from localhost ([127.0.0.1]:54191 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kPsZq-0007iO-DH for submit@debbugs.gnu.org; Tue, 06 Oct 2020 15:24:46 -0400 Received: from flashner.co.il ([178.62.234.194]:34078) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kPsZl-0007i8-3r for 43825@debbugs.gnu.org; Tue, 06 Oct 2020 15:24:45 -0400 Received: from localhost (unknown [31.210.181.177]) by flashner.co.il (Postfix) with ESMTPSA id D69BF4022E; Tue, 6 Oct 2020 19:24:34 +0000 (UTC) Date: Tue, 6 Oct 2020 22:23:59 +0300 From: Efraim Flashner To: Roel Janssen Subject: Re: [bug#43825] [PATCH] bioinformatics: htslib: Enable support for custom URI schemes. Message-ID: <20201006192359.GG21174@E5400> References: MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="p7qwJlK53pWzbayA" Content-Disposition: inline In-Reply-To: X-PGP-Key-ID: 0x41AAE7DCCA3D8351 X-PGP-Key: https://flashner.co.il/~efraim/efraim_flashner.asc X-PGP-Fingerprint: A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 43825 Cc: 43825@debbugs.gnu.org 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 (-) --p7qwJlK53pWzbayA Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Tue, Oct 06, 2020 at 10:48:31AM +0200, Roel Janssen wrote: > Dear Guix, >=20 > 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.=20 >=20 > Kind regards, > Roel Janssen >=20 That sounds fine to me. --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --p7qwJlK53pWzbayA Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAl98xE8ACgkQQarn3Mo9 g1GXfw/+OXGcLlQSMA9TOkZZAChx4UI+sV+Nhjv5mY/hMAc16ot/1YurWM/wRpyC Ta28LwzN/mc6Q/emqvZss9zdNFhHaczB6/s/muurbGpFsE81k3j75j9kXGIwMw1x OgSt6ghWMmRp+Nly8Ip5MjTkliV7UZJPO1o83FObKRAXUj/6YLHPyVrRLWAmN7+w NxqEl1pKOOGpi9Egcb9aHHwkw+vAP6o1gi8t/n1kfN8rs45oDi5AeAEoxQbveN3B hEtOlhRQan7Ey4f8ebDSSTGoH86PlRTPcDgR9VEWDZ13eRAWkNs4jlLh0eppzW5q iukHoxfSC4kIGp6elja/HuIj/QVA7De1fhL+BNem4hy0/W6gHCuw9o3j2PByTgDk rywknFyt9FFgCQMHZsTAmOSOHkOSzTbkox4gYU+0VLRs7RpRcyj6R7J9IsD4v4Ki j1hJKrJv8zWPSs6OJN8dHZrbdFvNmECb8qR0urKnYybhPnlFFv82cWcIUymsyPS5 ZIwGWdcXHJHUQ/CjovBfbrXq0byX6OAsN/Fo/ehh91wfF1B8Up6JPmPWRhg1xVvB BpaYBjrJTr0pyW3ITyDIYoxa/YcvpkjEK0MalWNABiB3Lo8rheDnyVbli8rvvmNz EDe9TMIf1HW/AUzrfsld1lQF6LXabvCW66etvoJ1RpyLwMO76jQ= =DMoz -----END PGP SIGNATURE----- --p7qwJlK53pWzbayA-- From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 06 16:54:38 2020 Received: (at 43825) by debbugs.gnu.org; 6 Oct 2020 20:54:39 +0000 Received: from localhost ([127.0.0.1]:54266 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kPtyo-0001NM-K6 for submit@debbugs.gnu.org; Tue, 06 Oct 2020 16:54:38 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21121) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kPtyl-0001NC-Vx for 43825@debbugs.gnu.org; Tue, 06 Oct 2020 16:54:37 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1602017665; cv=none; d=zohomail.com; s=zohoarc; b=S2pgh59CBek3MxU5RuxFRoYgdGoXjVApmGO7gSPrs/Hfor6FfIB66UUcyBJ8fesAhwO4y9E4G8BGtzcOSPEh8Gm+yxFgsv8PtxzYCYJfr3C3m/Q2jwznMrx+neQV600vTb8He9I9ZY2tZ6pOcDYd/zMquO5iEwrSbWzT9bgIIPg= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1602017665; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=BdEmCTl9HSxlJOTUKZ58VzhPKl6OlgmgXtxX9oJEGrw=; b=k3bWhqk7eR01g2G9sYV7ybmFi4ydQiKuLmb4qfjUqFqLyj0uJ4y4J7DqPDTH65GEAA9rt4BnVmSCk+s7hVTXSo6WbZi3XMJjR2aPxUX3U2MzC7Kt/9q49rPdb+C1eAQxB2uDuT0eA/vCilM15cSLJptuOQnX9iKoHDDWC8cDf6w= 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= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1602017665; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type; bh=BdEmCTl9HSxlJOTUKZ58VzhPKl6OlgmgXtxX9oJEGrw=; b=TCyHyYSXDrSFoPpv/uZOhsjFHkXm43FcA9xyoTtSyrH2FoEMl8+bv1YS95Q/EPxa runmxFejPM5AfRsZy+0xHdTj7OoVZvXRyuTgIK9a3I6okXugItQ4cGf8XHSZil7SyTd Q0CIAMdQJncsLHmFN2N7jmvzQrcqnyuoNjQhySYE= Received: from localhost (p4fd5aadc.dip0.t-ipconnect.de [79.213.170.220]) by mx.zohomail.com with SMTPS id 1602017663354504.86602596332045; Tue, 6 Oct 2020 13:54:23 -0700 (PDT) References: User-agent: mu4e 1.4.13; emacs 27.1 From: Ricardo Wurmus To: Roel Janssen Subject: Re: [bug#43825] [PATCH] bioinformatics: htslib: Enable support for custom URI schemes. In-reply-to: X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 06 Oct 2020 22:56:01 +0200 Message-ID: <87o8lfysym.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 43825 Cc: 43825@debbugs.gnu.org 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 (-) Hi Roel, > I'd like to apply this patch to enable accessing files stored in > certain "cloud" systems. Sounds good to me. Please move the explanation from the commit message to the code as a comment. As commit message please use: * gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support for custom URIs. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 07 09:37:26 2020 Received: (at 43825-done) by debbugs.gnu.org; 7 Oct 2020 13:37:26 +0000 Received: from localhost ([127.0.0.1]:55602 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQ9dF-00018j-UV for submit@debbugs.gnu.org; Wed, 07 Oct 2020 09:37:26 -0400 Received: from eggs.gnu.org ([209.51.188.92]:51258) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQ9dC-00018V-Ga for 43825-done@debbugs.gnu.org; Wed, 07 Oct 2020 09:37:24 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:44971) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kQ9d7-0005nF-0s; Wed, 07 Oct 2020 09:37:17 -0400 Received: from [143.121.198.62] (port=50310 helo=cog147) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kQ9d6-0005Uj-JV; Wed, 07 Oct 2020 09:37:16 -0400 Message-ID: <685d3a822d8c81c05073041d3e599a8ba7f4d5d1.camel@gnu.org> Subject: Re: [bug#43825] [PATCH] bioinformatics: htslib: Enable support for custom URI schemes. From: Roel Janssen To: Ricardo Wurmus Date: Wed, 07 Oct 2020 15:37:14 +0200 In-Reply-To: <87o8lfysym.fsf@elephly.net> References: <87o8lfysym.fsf@elephly.net> Content-Type: text/plain; charset="UTF-8" X-Mailer: Evolution 3.28.5-0ubuntu0.18.04.2 Mime-Version: 1.0 Content-Transfer-Encoding: 7bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 43825-done Cc: 43825-done@debbugs.gnu.org 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: -3.3 (---) On Tue, 2020-10-06 at 22:56 +0200, Ricardo Wurmus wrote: > Hi Roel, > > > I'd like to apply this patch to enable accessing files stored in > > certain "cloud" systems. > > Sounds good to me. Please move the explanation from the commit > message > to the code as a comment. > > As commit message please use: > > * gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support > for custom URIs. > Thank you! I've committed this patch at fb0037a. Kind regards, Roel Janssen From unknown Mon Aug 18 00:08:12 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 05 Nov 2020 12:24:04 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator