From unknown Sat Jun 21 05:17:06 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47930] [PATCH] gnu: Add pbgzip. Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 21 Apr 2021 12:28:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 47930 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47930@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.161900803421959 (code B ref -1); Wed, 21 Apr 2021 12:28:02 +0000 Received: (at submit) by debbugs.gnu.org; 21 Apr 2021 12:27:14 +0000 Received: from localhost ([127.0.0.1]:57131 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lZBwi-0005i1-Hk for submit@debbugs.gnu.org; Wed, 21 Apr 2021 08:27:14 -0400 Received: from lists.gnu.org ([209.51.188.17]:47738) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lZBwe-0005hr-S9 for submit@debbugs.gnu.org; Wed, 21 Apr 2021 08:27:07 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:49874) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lZBwd-0004le-5t for guix-patches@gnu.org; Wed, 21 Apr 2021 08:27:03 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:54810) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lZBwc-0001On-Kw for guix-patches@gnu.org; Wed, 21 Apr 2021 08:27:02 -0400 Received: from [143.121.198.253] (port=57430) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1lZBwX-0004Gt-8f for guix-patches@gnu.org; Wed, 21 Apr 2021 08:27:00 -0400 From: Roel Janssen Message-ID: Date: Wed, 21 Apr 2021 14:26:47 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.7.1 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="------------307951D33DB4D2430D3BCAC4" Content-Language: en-US X-Spam-Score: -2.3 (--) 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 (-) This is a multi-part message in MIME format. --------------307951D33DB4D2430D3BCAC4 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi Guix, Here's a patch to add pbgzip.  Lint complains that there is no release on the Github page, but there's nothing I can do about it. Kind regards, Roel Janssen --------------307951D33DB4D2430D3BCAC4 Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-Add-pbgzip.patch" Content-Transfer-Encoding: 8bit Content-Disposition: attachment; filename="0001-gnu-Add-pbgzip.patch" >From 3d34e82ee67f5ee0b226de350f40d7f881169a56 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 21 Apr 2021 14:24:07 +0200 Subject: [PATCH] gnu: Add pbgzip. * gnu/packages/bioinformatics.scm (pbgzip): New variable. --- gnu/packages/bioinformatics.scm | 42 ++++++++++++++++++++++++++++++++- 1 file changed, 41 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 31205c473a..35601378c2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins ;;; Copyright © 2015 Andreas Enge -;;; Copyright © 2016, 2020 Roel Janssen +;;; Copyright © 2016, 2020, 2021 Roel Janssen ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner ;;; Copyright © 2016, 2020 Marius Bakke ;;; Copyright © 2016, 2018 Raoul Bonnal @@ -569,6 +569,46 @@ input and output BAMs must adhere to the PacBio BAM format specification. Non-PacBio BAMs will cause exceptions to be thrown.") (license license:bsd-3))) +(define-public pbgzip + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) + (package + (name "pbgzip") + (version (string-take commit 7)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nh13/pbgzip") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'autogen + (lambda _ + (zero? (system* "sh" "autogen.sh"))))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/nh13/pbgzip") + (synopsis "Parallel Block GZIP") + (description "This package implements parallel block gzip. For many +formats, in particular genomics data formats, data are compressed in +fixed-length blocks such that they can be easily indexed based on a (genomic) +coordinate order, since typically each block is sorted according to this order. +This allows for each block to be individually compressed (deflated), or more +importantly, decompressed (inflated), with the latter enabling random retrieval +of data in large files (gigabytes to terabytes). @code{pbgzip} is not limited +to any particular format, but certain features are tailored to genomics data +formats when enabled. Parallel decompression is somewhat faster, but truly the +speedup comes during compression.") + (license license:expat)))) + (define-public blasr-libcpp (package (name "blasr-libcpp") -- 2.31.1 --------------307951D33DB4D2430D3BCAC4-- From unknown Sat Jun 21 05:17:06 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47930] [PATCH] gnu: Add pbgzip. Resent-From: Xinglu Chen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 21 Apr 2021 21:45:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47930 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Roel Janssen , 47930@debbugs.gnu.org Received: via spool by 47930-submit@debbugs.gnu.org id=B47930.161904150121536 (code B ref 47930); Wed, 21 Apr 2021 21:45:02 +0000 Received: (at 47930) by debbugs.gnu.org; 21 Apr 2021 21:45:01 +0000 Received: from localhost ([127.0.0.1]:59958 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lZKeZ-0005bF-Dx for submit@debbugs.gnu.org; Wed, 21 Apr 2021 17:45:01 -0400 Received: from h87-96-130-155.cust.a3fiber.se ([87.96.130.155]:40008 helo=mail.yoctocell.xyz) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lZKeV-0005b0-N7 for 47930@debbugs.gnu.org; Wed, 21 Apr 2021 17:44:58 -0400 From: Xinglu Chen DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=yoctocell.xyz; s=mail; t=1619041489; bh=YOulrT5SdjLOzvrd1nDDQ6wYo7O3gsSzQohu59tOMUE=; h=From:To:Subject:In-Reply-To:References:Date; b=o9p0NashWLcDtBvndM5lf5CXPGuAvY9UIET+bCGeDGxiHbXLxOBO3tBPBP5cPyEd1 fZIZxUJqloCKfF+jbVWREUZysdsF9FgfDLq4Y7OV2qHo9wLfdrkgzZdjyXsTJUls8Z F8ER+6HBBYrlMf0P7/PPym/DGMOhmbunUW86MsN8= In-Reply-To: References: Date: Wed, 21 Apr 2021 23:44:48 +0200 Message-ID: <875z0f71nz.fsf@yoctocell.xyz> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 2.6 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: On Wed, Apr 21 2021, Roel Janssen wrote: > * gnu/packages/bioinformatics.scm (pbgzip): New variable. > > [...] > > +(define-public pbgzip > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > + (package > + (name "pbgzip") > + (ve [...] Content analysis details: (2.6 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 2.0 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: yoctocell.xyz (xyz)] -0.0 SPF_PASS SPF: sender matches SPF record 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 0.2 FROM_SUSPICIOUS_NTLD From abused NTLD 0.4 RDNS_DYNAMIC Delivered to internal network by host with dynamic-looking rDNS 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: 2.6 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: On Wed, Apr 21 2021, Roel Janssen wrote: > * gnu/packages/bioinformatics.scm (pbgzip): New variable. > > [...] > > +(define-public pbgzip > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > + (package > + (name "pbgzip") > + (ve [...] Content analysis details: (2.6 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 2.0 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: yoctocell.xyz (xyz)] -0.0 SPF_PASS SPF: sender matches SPF record 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 0.2 FROM_SUSPICIOUS_NTLD From abused NTLD -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager 1.0 BULK_RE_SUSP_NTLD Precedence bulk and RE: from a suspicious TLD 0.4 RDNS_DYNAMIC Delivered to internal network by host with dynamic-looking rDNS --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable On Wed, Apr 21 2021, Roel Janssen wrote: > * gnu/packages/bioinformatics.scm (pbgzip): New variable. > > [...] >=20=20 > +(define-public pbgzip > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > + (package > + (name "pbgzip") > + (version (string-take commit 7)) I think using (git-version VERSION REVISION COMMIT) is preferred. Something like (git-version "0.0.0" "0" commit). > + (source (origin > + (method git-fetch) > + (uri (git-reference > + (url "https://github.com/nh13/pbgzip") > + (commit commit))) > + (file-name (string-append name "-" version)) Use (git-file-name name version). > + (sha256 > + (base32 > + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"= )))) > + (build-system gnu-build-system) > + (arguments > + `(#:phases > + (modify-phases %standard-phases > + (add-after 'unpack 'autogen > + (lambda _ > + (zero? (system* "sh" "autogen.sh"))))))) IIRC, phases don=E2=80=99t have to return #t, so you could remove =E2=80=98= zero?=E2=80=99. Builds fine, but I haven=E2=80=99t tested it. --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQJJBAEBCAAzFiEEAVhh4yyK5+SEykIzrPUJmaL7XHkFAmCAnNAVHHB1YmxpY0B5 b2N0b2NlbGwueHl6AAoJEKz1CZmi+1x5gzoP/ix8CAlbjDKcYjkIWPg4sn9CMnrp iY9N/AqBRf/gdLr8uBLIryClg/9MK6ihpLzFxn0Aa9Ildbn/kEl40OjfSfhap5lP d8N/HHaJuXd6JY6xF9xi/Nd24/Uzjg0hXO1pUFYJdq6JhYGkIFaZfBDgpUvKi51b a0pl3Nh511RnevAN9flHpdY0sso/QXYEyYo7fIOY7XPxstpjd0yYtdunmxSgsUb4 Lt9FhqzYcVMZYAbBCdn3PYQ/sV3XQbemdmf0+BtDTe2h35AT9u4ShhucF4xeFq/n zTIptWkZXQFCU6VdkTHka905ltuqiCPk7bxfPC2Q8wBDMlwHa9SVoakuQbFlC83C dZ/qFVukImnGSIn3DRWVD9OY0zlJQA4uqZbmjvIkV6fy+QDEnDDs0BMV8hfajzZY NjT4RFNWVn7554P1AGEGkRDKbeRia61laHnpBYhvgCWZmHlEcxDcVtvrqg/g/B4F ErZRQo71iLZ09MzebDefDq98JjLt0OAqmb8bsZ+Iav8WyIBz1JUqM06ySwq+DksC bvfjiF19zz40Rp1PxkeAzVEIuIeCu6NX4vWq2LInAZQMy1JamscA53aRHXJCu7p5 RhK4goD70bwK5FakduxEBM7K83eR3UG3bd/Jyyzff08bbuhGxD6r/en+hicQZD8G dzlOM36nbDONq8OR =lCr3 -----END PGP SIGNATURE----- --=-=-=-- From unknown Sat Jun 21 05:17:06 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47930] [PATCH] gnu: Add pbgzip. Resent-From: Xinglu Chen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 21 Apr 2021 21:46:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47930 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Roel Janssen , 47930@debbugs.gnu.org Received: via spool by 47930-submit@debbugs.gnu.org id=B47930.161904151921626 (code B ref 47930); Wed, 21 Apr 2021 21:46:01 +0000 Received: (at 47930) by debbugs.gnu.org; 21 Apr 2021 21:45:19 +0000 Received: from localhost ([127.0.0.1]:59966 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lZKer-0005cj-OQ for submit@debbugs.gnu.org; Wed, 21 Apr 2021 17:45:19 -0400 Received: from h87-96-130-155.cust.a3fiber.se ([87.96.130.155]:40022 helo=mail.yoctocell.xyz) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lZKel-0005cL-S1 for 47930@debbugs.gnu.org; Wed, 21 Apr 2021 17:45:16 -0400 From: Xinglu Chen DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=yoctocell.xyz; s=mail; t=1619041506; bh=SS5Ogf8+T4I5hBvO3iVpCbmuVp8ebl4dRZ/oO5X8z0w=; h=From:To:Subject:In-Reply-To:References:Date; b=WheI20Oh4M46e5v722VnmYea8LRHEdfuLZ1h1mUZEMentmyccya2od+Kdi5gYYh3S 1Qg0cX0ASwFgfoNomoHls7fyJBoBQxHhZcquNi9owz3qgaNdQSU+RByjQwi3OQfkDR Y6mJhKD5694ZlMslzs22KJj+KKrOSphbMYrbTHfo= In-Reply-To: References: Date: Wed, 21 Apr 2021 23:45:05 +0200 Message-ID: <874kfz71ni.fsf@yoctocell.xyz> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 2.6 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: On Wed, Apr 21 2021, Roel Janssen wrote: > * gnu/packages/bioinformatics.scm (pbgzip): New variable. > > [...] > > +(define-public pbgzip > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > + (package > + (name "pbgzip") > + (ve [...] Content analysis details: (2.6 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 2.0 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: yoctocell.xyz (xyz)] -0.0 SPF_PASS SPF: sender matches SPF record 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 0.2 FROM_SUSPICIOUS_NTLD From abused NTLD 0.4 RDNS_DYNAMIC Delivered to internal network by host with dynamic-looking rDNS 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: 2.6 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: On Wed, Apr 21 2021, Roel Janssen wrote: > * gnu/packages/bioinformatics.scm (pbgzip): New variable. > > [...] > > +(define-public pbgzip > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > + (package > + (name "pbgzip") > + (ve [...] Content analysis details: (2.6 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 2.0 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: yoctocell.xyz (xyz)] -0.0 SPF_PASS SPF: sender matches SPF record 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 0.2 FROM_SUSPICIOUS_NTLD From abused NTLD -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager 1.0 BULK_RE_SUSP_NTLD Precedence bulk and RE: from a suspicious TLD 0.4 RDNS_DYNAMIC Delivered to internal network by host with dynamic-looking rDNS On Wed, Apr 21 2021, Roel Janssen wrote: > * gnu/packages/bioinformatics.scm (pbgzip): New variable. > > [...] >=20=20 > +(define-public pbgzip > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > + (package > + (name "pbgzip") > + (version (string-take commit 7)) I think using (git-version VERSION REVISION COMMIT) is preferred. Something like (git-version "0.0.0" "0" commit). > + (source (origin > + (method git-fetch) > + (uri (git-reference > + (url "https://github.com/nh13/pbgzip") > + (commit commit))) > + (file-name (string-append name "-" version)) Use (git-file-name name version). > + (sha256 > + (base32 > + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"= )))) > + (build-system gnu-build-system) > + (arguments > + `(#:phases > + (modify-phases %standard-phases > + (add-after 'unpack 'autogen > + (lambda _ > + (zero? (system* "sh" "autogen.sh"))))))) IIRC, phases don=E2=80=99t have to return #t, so you could remove =E2=80=98= zero?=E2=80=99. Builds fine, but I haven=E2=80=99t tested it. From unknown Sat Jun 21 05:17:06 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47930] [PATCH] gnu: Add pbgzip. Resent-From: Maxime Devos Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 22 Apr 2021 16:41:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47930 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Xinglu Chen , Roel Janssen , 47930@debbugs.gnu.org Received: via spool by 47930-submit@debbugs.gnu.org id=B47930.161910966022595 (code B ref 47930); Thu, 22 Apr 2021 16:41:02 +0000 Received: (at 47930) by debbugs.gnu.org; 22 Apr 2021 16:41:00 +0000 Received: from localhost ([127.0.0.1]:35394 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lZcNu-0005sM-4Y for submit@debbugs.gnu.org; Thu, 22 Apr 2021 12:40:59 -0400 Received: from laurent.telenet-ops.be ([195.130.137.89]:32862) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lZcNq-0005sB-Tu for 47930@debbugs.gnu.org; Thu, 22 Apr 2021 12:40:57 -0400 Received: from ptr-bvsjgyjmffd7q9timvx.18120a2.ip6.access.telenet.be ([IPv6:2a02:1811:8c09:9d00:aaf1:9810:a0b8:a55d]) by laurent.telenet-ops.be with bizsmtp id vsgs2400J0mfAB401sgsbn; Thu, 22 Apr 2021 18:40:53 +0200 Message-ID: From: Maxime Devos Date: Thu, 22 Apr 2021 18:40:46 +0200 In-Reply-To: <874kfz71ni.fsf@yoctocell.xyz> References: <874kfz71ni.fsf@yoctocell.xyz> Content-Type: multipart/signed; micalg="pgp-sha512"; protocol="application/pgp-signature"; boundary="=-F+xkGPI0qS6QPRs4F+js" User-Agent: Evolution 3.34.2 MIME-Version: 1.0 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=telenet.be; s=r21; t=1619109653; bh=5EsT6hBgwe2ckNOve4t8ftlh6qxgkynMrNsOPgf6bEY=; h=Subject:From:To:Date:In-Reply-To:References; b=MUHsiGxqL0eJxSXgNRuSkaXlYEpGTOpYVIl4jcNZ1Y5A4KwwOUGlCyWeGxP84iwO0 gnYIFOf1heKUpDeKURCSB2eaJ7Y/7vo2P4NTTckWW0DsaSMy0QhBuaTi9JhdND4DH1 5LdPG9t0z40mIDFR4jYF/HxeXF0prsQr45Rohset65Z/IcmRuQ8wKBdBUi0GevQ2e2 z/y83rRKSurT8dR2bIVji/8NnmthIqhyc3X/bTAnoljYBvsJLo47H7kj8Vzi6bhP70 1904jsKFnwH6Ng7318jxzuP0COfhfSFNwX0l/sQJfaLpV0MWbPcQirwBHzJAII1Srf 7BO5PRqhOD/Uw== X-Spam-Score: -0.7 (/) 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: -1.7 (-) --=-F+xkGPI0qS6QPRs4F+js Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Xinglu Chen schreef op wo 21-04-2021 om 23:45 [+0200]: > On Wed, Apr 21 2021, Roel Janssen wrote: >=20 > > [...] > > + (arguments > > + `(#:phases > > + (modify-phases %standard-phases > > + (add-after 'unpack 'autogen > > + (lambda _ > > + (zero? (system* "sh" "autogen.sh"))))))) >=20 > IIRC, phases don=E2=80=99t have to return #t, so you could remove =E2=80= =98zero?=E2=80=99. Try running (system* "does-not-exist"). It will fail by returning something non-zero. If I recall how to call "invoke" correctly, I would recommend (invoke "sh" "autogen.sh") here. "invoke" raises an exception when the command fails, instead of returning something. Greetings, Maxime. --=-F+xkGPI0qS6QPRs4F+js Content-Type: application/pgp-signature; name="signature.asc" Content-Description: This is a digitally signed message part Content-Transfer-Encoding: 7bit -----BEGIN PGP SIGNATURE----- iI0EABYKADUWIQTB8z7iDFKP233XAR9J4+4iGRcl7gUCYIGnDhccbWF4aW1lZGV2 b3NAdGVsZW5ldC5iZQAKCRBJ4+4iGRcl7onhAP4lw3JsxMrS3hVpGd7NA5OU/MXV +UbQEMCLHcydR3OQ0wEA9DQz9+i3E3/XgCGhdELKcSxuV+5N1rqygNC6UtolbAk= =oB8m -----END PGP SIGNATURE----- --=-F+xkGPI0qS6QPRs4F+js-- From unknown Sat Jun 21 05:17:06 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47930] [PATCH] gnu: Add pbgzip. Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 29 Apr 2021 07:30:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47930 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Maxime Devos Cc: Xinglu Chen , 47930@debbugs.gnu.org, Roel Janssen Received: via spool by 47930-submit@debbugs.gnu.org id=B47930.161968139813623 (code B ref 47930); Thu, 29 Apr 2021 07:30:02 +0000 Received: (at 47930) by debbugs.gnu.org; 29 Apr 2021 07:29:58 +0000 Received: from localhost ([127.0.0.1]:54705 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lc17U-0003Xe-HM for submit@debbugs.gnu.org; Thu, 29 Apr 2021 03:29:58 -0400 Received: from flashner.co.il ([178.62.234.194]:54272) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lc17Q-0003XL-HW for 47930@debbugs.gnu.org; Thu, 29 Apr 2021 03:29:54 -0400 Received: from localhost (unknown [31.210.177.125]) by flashner.co.il (Postfix) with ESMTPSA id 871BB401FA; Thu, 29 Apr 2021 07:29:46 +0000 (UTC) Date: Thu, 29 Apr 2021 10:29:44 +0300 From: Efraim Flashner Message-ID: Mail-Followup-To: Efraim Flashner , Maxime Devos , Xinglu Chen , Roel Janssen , 47930@debbugs.gnu.org References: <874kfz71ni.fsf@yoctocell.xyz> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="1S/H/dc6MxbqvX2j" 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-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 (-) --1S/H/dc6MxbqvX2j Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Thu, Apr 22, 2021 at 06:40:46PM +0200, Maxime Devos wrote: > Xinglu Chen schreef op wo 21-04-2021 om 23:45 [+0200]: > > On Wed, Apr 21 2021, Roel Janssen wrote: > >=20 > > > [...] > > > + (arguments > > > + `(#:phases > > > + (modify-phases %standard-phases > > > + (add-after 'unpack 'autogen > > > + (lambda _ > > > + (zero? (system* "sh" "autogen.sh"))))))) > >=20 > > IIRC, phases don=E2=80=99t have to return #t, so you could remove =E2= =80=98zero?=E2=80=99. >=20 > Try running (system* "does-not-exist"). It will fail by returning > something non-zero. If I recall how to call "invoke" correctly, > I would recommend (invoke "sh" "autogen.sh") here. "invoke" raises > an exception when the command fails, instead of returning something. While we're at it, can this phase replace 'bootstrap? It seems to me we shouldn't need both phases. --=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 --1S/H/dc6MxbqvX2j Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAmCKYGUACgkQQarn3Mo9 g1ENrxAAn0JbKu8WcZUoA6IZtbkbQJWGcoOILW0KwjLxOky1rgWh7kMPtGvRBs/e Y8ISNoxfnnwdaRSacxDzlL9VAaMNAtcHYVdfhlKRMG/Uhg0F2EwyvjTDmpTLUWEg jjlfkFLaM2P1hgvsSGKciLpLgL9xgDZ0hSSQGMs+hAjBzpzroeK6l/tLEgqWbFLb PLN/fcNfVuGOum5PAObxuicWZQJzxwKKvksiDaxsP9CZ/Zb2jI1IIi6HT8P4G0Pq x6XeAHX5XVVNuK+PUFATG6RG1uX3wfN3BIHScQNl0KL6vknBBquE/AoJ8sT1DOcj aQDLkHnIAPYsKB/pi+G9N1B9XGJqmQsRvfjff57k5cvyNGyqHDW82BS7HOwWRW6f H1htinWn7LHShFR3sc23oM+pBTvshN26CtAYdOIoq0t+Sp3P5tYw8ADIlBHSjRC+ vDDHXkYt5F+iYYOljviGLA7Wq58xUEgEcaN+y0zrr+/YLFLAUwiRYMsjz7Bb0YyT /TAuDrV6YWwHfddBUXZeCYajGRloes2XL1ossO317emnRaceWPhSWzPWAoTAEy5S M5ETAyrrIGIdZdc1CzW+O3wzdunTgTvTQXtKvuacKm3eFsz9twlNQias6dzh3eiG 4/HfU7PbWQtM1WtvwMWqYt+1kHWjukeCzobmlsXQoou1GUZgZog= =GAp0 -----END PGP SIGNATURE----- --1S/H/dc6MxbqvX2j-- From unknown Sat Jun 21 05:17:06 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47930] [PATCH] gnu: Add pbgzip. Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 29 Apr 2021 12:24:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47930 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Efraim Flashner , Maxime Devos , Xinglu Chen Cc: 47930@debbugs.gnu.org Received: via spool by 47930-submit@debbugs.gnu.org id=B47930.161969898519581 (code B ref 47930); Thu, 29 Apr 2021 12:24:02 +0000 Received: (at 47930) by debbugs.gnu.org; 29 Apr 2021 12:23:05 +0000 Received: from localhost ([127.0.0.1]:55025 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lc5h6-00055E-Ag for submit@debbugs.gnu.org; Thu, 29 Apr 2021 08:23:05 -0400 Received: from eggs.gnu.org ([209.51.188.92]:35872) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lc5h3-000551-O0 for 47930@debbugs.gnu.org; Thu, 29 Apr 2021 08:22:59 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:41206) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lc5gw-0000VY-K5; Thu, 29 Apr 2021 08:22:50 -0400 Received: from [143.121.198.253] (port=58448) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1lc5gv-0001QS-EF; Thu, 29 Apr 2021 08:22:49 -0400 References: <874kfz71ni.fsf@yoctocell.xyz> From: Roel Janssen Message-ID: Date: Thu, 29 Apr 2021 14:22:43 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.7.1 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/mixed; boundary="------------3983BCA2AADF705861EDBE2F" Content-Language: en-US X-Spam-Score: -2.3 (--) 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 (---) This is a multi-part message in MIME format. --------------3983BCA2AADF705861EDBE2F Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit On 4/29/21 9:29 AM, Efraim Flashner wrote: > On Thu, Apr 22, 2021 at 06:40:46PM +0200, Maxime Devos wrote: >> Xinglu Chen schreef op wo 21-04-2021 om 23:45 [+0200]: >>> On Wed, Apr 21 2021, Roel Janssen wrote: >>> >>>> [...] >>>> + (arguments >>>> + `(#:phases >>>> + (modify-phases %standard-phases >>>> + (add-after 'unpack 'autogen >>>> + (lambda _ >>>> + (zero? (system* "sh" "autogen.sh"))))))) >>> IIRC, phases don’t have to return #t, so you could remove ‘zero?’. >> Try running (system* "does-not-exist"). It will fail by returning >> something non-zero. If I recall how to call "invoke" correctly, >> I would recommend (invoke "sh" "autogen.sh") here. "invoke" raises >> an exception when the command fails, instead of returning something. > While we're at it, can this phase replace 'bootstrap? It seems to me we > shouldn't need both phases. This indeed seems to be the best thing to do.  I attached a new patch. I had to leave autoconf and automake in the native-inputs because otherwise the command "aclocal" and "autom4te" couldn't be found. Thanks all for the feedback!  I hope this new patch is fine. Kind regards, Roel Janssen --------------3983BCA2AADF705861EDBE2F Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-Add-pbgzip.patch" Content-Transfer-Encoding: 8bit Content-Disposition: attachment; filename="0001-gnu-Add-pbgzip.patch" >From b03f8d8926cdd6a28502f2bdc6db74854144f050 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 29 Apr 2021 14:18:30 +0200 Subject: [PATCH] gnu: Add pbgzip. * gnu/packages/bioinformatics.scm (pbgzip): New variable. --- gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++- 1 file changed, 35 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 83ebfc2d8f..8c4d0fc649 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins ;;; Copyright © 2015 Andreas Enge -;;; Copyright © 2016, 2020 Roel Janssen +;;; Copyright © 2016, 2020, 2021 Roel Janssen ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner ;;; Copyright © 2016, 2020 Marius Bakke ;;; Copyright © 2016, 2018 Raoul Bonnal @@ -571,6 +571,40 @@ input and output BAMs must adhere to the PacBio BAM format specification. Non-PacBio BAMs will cause exceptions to be thrown.") (license license:bsd-3))) +(define-public pbgzip + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) + (package + (name "pbgzip") + (version (string-take commit 7)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nh13/pbgzip") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/nh13/pbgzip") + (synopsis "Parallel Block GZIP") + (description "This package implements parallel block gzip. For many +formats, in particular genomics data formats, data are compressed in +fixed-length blocks such that they can be easily indexed based on a (genomic) +coordinate order, since typically each block is sorted according to this order. +This allows for each block to be individually compressed (deflated), or more +importantly, decompressed (inflated), with the latter enabling random retrieval +of data in large files (gigabytes to terabytes). @code{pbgzip} is not limited +to any particular format, but certain features are tailored to genomics data +formats when enabled. Parallel decompression is somewhat faster, but truly the +speedup comes during compression.") + (license license:expat)))) + (define-public blasr-libcpp (package (name "blasr-libcpp") -- 2.31.1 --------------3983BCA2AADF705861EDBE2F-- From unknown Sat Jun 21 05:17:06 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47930] [PATCH] gnu: Add pbgzip. Resent-From: Xinglu Chen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 30 Apr 2021 08:31:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47930 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Roel Janssen , Efraim Flashner , Maxime Devos Cc: 47930@debbugs.gnu.org Received: via spool by 47930-submit@debbugs.gnu.org id=B47930.161977145920883 (code B ref 47930); Fri, 30 Apr 2021 08:31:01 +0000 Received: (at 47930) by debbugs.gnu.org; 30 Apr 2021 08:30:59 +0000 Received: from localhost ([127.0.0.1]:57445 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lcOY7-0005Ql-DU for submit@debbugs.gnu.org; Fri, 30 Apr 2021 04:30:59 -0400 Received: from h87-96-130-155.cust.a3fiber.se ([87.96.130.155]:38360 helo=mail.yoctocell.xyz) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lcOY6-0005QY-G4 for 47930@debbugs.gnu.org; Fri, 30 Apr 2021 04:30:58 -0400 From: Xinglu Chen DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=yoctocell.xyz; s=mail; t=1619771451; bh=s7WAIDZNeJBjg9tHQzhLkVhU/TS7SldLLyQVayEs8C8=; h=From:To:Cc:Subject:In-Reply-To:References:Date; b=DyKtEvzeb1yDCe3PJzGAnZE2jRkDtU6tT25IvUq3PscIAYcuY2Ty1be7ie+YlWoDQ B8V302mv50QrOj73a0mtj7Pb3ltnSzxEWm5IH2Upq9C8Qd+mb6ymaqrJcDbp/CVAYa D9/qldR1lt36dquT1Bwe8HzvyVQzYx0/CnxFyU5o= In-Reply-To: References: <874kfz71ni.fsf@yoctocell.xyz> Date: Fri, 30 Apr 2021 10:30:49 +0200 Message-ID: <87czucnphi.fsf@yoctocell.xyz> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 2.9 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: On Thu, Apr 29 2021, Roel Janssen wrote: > +(define-public pbgzip > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > + (package > + (name "pbgzip") > + (version (string-take commit 7)) Maybe you missed my previous suggestions? Content analysis details: (2.9 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 2.0 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: yoctocell.xyz (xyz)] -0.0 SPF_PASS SPF: sender matches SPF record 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 0.4 RDNS_DYNAMIC Delivered to internal network by host with dynamic-looking rDNS 0.5 FROM_SUSPICIOUS_NTLD From abused NTLD 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: 2.9 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: On Thu, Apr 29 2021, Roel Janssen wrote: > +(define-public pbgzip > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > + (package > + (name "pbgzip") > + (version (string-take commit 7)) Maybe you missed my previous suggestions? Content analysis details: (2.9 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 2.0 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: yoctocell.xyz (xyz)] -0.0 SPF_PASS SPF: sender matches SPF record 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 1.0 BULK_RE_SUSP_NTLD Precedence bulk and RE: from a suspicious TLD 0.4 RDNS_DYNAMIC Delivered to internal network by host with dynamic-looking rDNS 0.5 FROM_SUSPICIOUS_NTLD From abused NTLD -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager On Thu, Apr 29 2021, Roel Janssen wrote: > +(define-public pbgzip > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > + (package > + (name "pbgzip") > + (version (string-take commit 7)) Maybe you missed my previous suggestions? https://issues.guix.gnu.org/47930#2 =20=20 > + (source (origin > + (method git-fetch) > + (uri (git-reference > + (url "https://github.com/nh13/pbgzip") > + (commit commit))) > + (file-name (string-append name "-" version)) > + (sha256 > + (base32 > + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"= )))) > + (build-system gnu-build-system) > + (native-inputs > + `(("autoconf" ,autoconf) > + ("automake" ,automake))) > + (inputs > + `(("zlib" ,zlib))) > + (home-page "https://github.com/nh13/pbgzip") > + (synopsis "Parallel Block GZIP") > + (description "This package implements parallel block gzip. For ma= ny > +formats, in particular genomics data formats, data are compressed in > +fixed-length blocks such that they can be easily indexed based on a (gen= omic) > +coordinate order, since typically each block is sorted according to this= order. > +This allows for each block to be individually compressed (deflated), or = more > +importantly, decompressed (inflated), with the latter enabling random re= trieval > +of data in large files (gigabytes to terabytes). @code{pbgzip} is not l= imited > +to any particular format, but certain features are tailored to genomics = data > +formats when enabled. Parallel decompression is somewhat faster, but tr= uly the ^^^^^^= ^^^^^^^ > +speedup comes during compression.") ^^^^^^^ =E2=80=9Cbut the true speedup=E2=80=9D instead? From unknown Sat Jun 21 05:17:06 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#47930] [PATCH] gnu: Add pbgzip. Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 30 Apr 2021 11:50:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47930 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Xinglu Chen , Efraim Flashner , Maxime Devos Cc: 47930@debbugs.gnu.org Received: via spool by 47930-submit@debbugs.gnu.org id=B47930.161978334625303 (code B ref 47930); Fri, 30 Apr 2021 11:50:01 +0000 Received: (at 47930) by debbugs.gnu.org; 30 Apr 2021 11:49:06 +0000 Received: from localhost ([127.0.0.1]:57679 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lcRdl-0006Zz-TG for submit@debbugs.gnu.org; Fri, 30 Apr 2021 07:49:06 -0400 Received: from eggs.gnu.org ([209.51.188.92]:38184) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lcRdj-0006ZV-Ob for 47930@debbugs.gnu.org; Fri, 30 Apr 2021 07:49:00 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:42837) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lcRdd-0007h7-2J; Fri, 30 Apr 2021 07:48:53 -0400 Received: from 2001-1c02-0b18-2900-222e-248e-9586-e52d.cable.dynamic.v6.ziggo.nl ([2001:1c02:b18:2900:222e:248e:9586:e52d]:46314) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1lcRdc-0003nY-FJ; Fri, 30 Apr 2021 07:48:52 -0400 Message-ID: <052ee880cea08e4e1627a2181f7173ab9587b6c8.camel@gnu.org> From: Roel Janssen Date: Fri, 30 Apr 2021 13:48:48 +0200 In-Reply-To: <87czucnphi.fsf@yoctocell.xyz> References: <874kfz71ni.fsf@yoctocell.xyz> <87czucnphi.fsf@yoctocell.xyz> Content-Type: multipart/mixed; boundary="=-aMPWy4UXcvpu5IepufA7" User-Agent: Evolution 3.40.0 (3.40.0-1.fc34) MIME-Version: 1.0 X-Spam-Score: -2.3 (--) 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 (-) --=-aMPWy4UXcvpu5IepufA7 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit On Fri, 2021-04-30 at 10:30 +0200, Xinglu Chen wrote: > On Thu, Apr 29 2021, Roel Janssen wrote: > > > +(define-public pbgzip > > +  (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > > +    (package > > +      (name "pbgzip") > > +      (version (string-take commit 7)) > > Maybe you missed my previous suggestions? > >   https://issues.guix.gnu.org/47930#2 > I'm sorry, I forgot to adapt. >   > > +      (source (origin > > +                (method git-fetch) > > +                (uri (git-reference > > +                      (url "https://github.com/nh13/pbgzip") > > +                      (commit commit))) > > +                (file-name (string-append name "-" version)) > > +                (sha256 > > +                 (base32 > > +                  > > "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd")))) > > +      (build-system gnu-build-system) > > +      (native-inputs > > +       `(("autoconf" ,autoconf) > > +         ("automake" ,automake))) > > +      (inputs > > +       `(("zlib" ,zlib))) > > +      (home-page "https://github.com/nh13/pbgzip") > > +      (synopsis "Parallel Block GZIP") > > +      (description "This package implements parallel block gzip.  > > For many > > +formats, in particular genomics data formats, data are compressed > > in > > +fixed-length blocks such that they can be easily indexed based on > > a (genomic) > > +coordinate order, since typically each block is sorted according > > to this order. > > +This allows for each block to be individually compressed > > (deflated), or more > > +importantly, decompressed (inflated), with the latter enabling > > random retrieval > > +of data in large files (gigabytes to terabytes).  @code{pbgzip} is > > not limited > > +to any particular format, but certain features are tailored to > > genomics data > > +formats when enabled.  Parallel decompression is somewhat faster, > > but truly the >                                                                      > ^^^^^^^^^^^^^ > > +speedup comes during compression.") >    ^^^^^^^ > > “but the true speedup” instead? Sure. I usually don't change descriptions as given by the creators of the software, but I applied your suggestion. Thank you for the elaborate suggestions! 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Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 30 Apr 2021 11:54:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47930 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Roel Janssen Cc: Maxime Devos , Xinglu Chen , 47930@debbugs.gnu.org Received: via spool by 47930-submit@debbugs.gnu.org id=B47930.161978363625762 (code B ref 47930); Fri, 30 Apr 2021 11:54:01 +0000 Received: (at 47930) by debbugs.gnu.org; 30 Apr 2021 11:53:56 +0000 Received: from localhost ([127.0.0.1]:57688 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lcRiS-0006hO-QX for submit@debbugs.gnu.org; Fri, 30 Apr 2021 07:53:56 -0400 Received: from flashner.co.il ([178.62.234.194]:58574) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lcRiQ-0006hB-Af for 47930@debbugs.gnu.org; Fri, 30 Apr 2021 07:53:51 -0400 Received: from localhost (unknown [31.210.177.125]) by flashner.co.il (Postfix) with ESMTPSA id 2EF24400AC; Fri, 30 Apr 2021 11:53:44 +0000 (UTC) Date: Fri, 30 Apr 2021 14:53:41 +0300 From: Efraim Flashner Message-ID: Mail-Followup-To: Efraim Flashner , Roel Janssen , Xinglu Chen , Maxime Devos , 47930@debbugs.gnu.org References: <874kfz71ni.fsf@yoctocell.xyz> <87czucnphi.fsf@yoctocell.xyz> <052ee880cea08e4e1627a2181f7173ab9587b6c8.camel@gnu.org> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="saCnEgrzqfQvnK7S" Content-Disposition: inline In-Reply-To: <052ee880cea08e4e1627a2181f7173ab9587b6c8.camel@gnu.org> 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-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 (-) --saCnEgrzqfQvnK7S Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Fri, Apr 30, 2021 at 01:48:48PM +0200, Roel Janssen wrote: > On Fri, 2021-04-30 at 10:30 +0200, Xinglu Chen wrote: > > On Thu, Apr 29 2021, Roel Janssen wrote: > >=20 > > > +(define-public pbgzip > > > +=C2=A0 (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > > > +=C2=A0=C2=A0=C2=A0 (package > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (name "pbgzip") > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (version (string-take commit 7)) > >=20 > > Maybe you missed my previous suggestions? > >=20 > > =C2=A0 https://issues.guix.gnu.org/47930#2 > >=20 >=20 > I'm sorry, I forgot to adapt. > > =C2=A0=20 > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (source (origin > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 (method git-fetch) > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 (uri (git-reference > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (url "https://= github.com/nh13/pbgzip") > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (commit commit= ))) > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 (file-name (string-append name "-" version)) > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 (sha256 > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (base32 > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 > > > "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd")))) > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (build-system gnu-build-system) > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (native-inputs > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 `(("autoconf" ,autoconf) > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 ("automake" ,automa= ke))) > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (inputs > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 `(("zlib" ,zlib))) > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (home-page "https://github.com/nh13/p= bgzip") > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (synopsis "Parallel Block GZIP") > > > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (description "This package implements= parallel block gzip.=C2=A0 > > > For many > > > +formats, in particular genomics data formats, data are compressed > > > in > > > +fixed-length blocks such that they can be easily indexed based on > > > a (genomic) > > > +coordinate order, since typically each block is sorted according > > > to this order. > > > +This allows for each block to be individually compressed > > > (deflated), or more > > > +importantly, decompressed (inflated), with the latter enabling > > > random retrieval > > > +of data in large files (gigabytes to terabytes).=C2=A0 @code{pbgzip}= is > > > not limited > > > +to any particular format, but certain features are tailored to > > > genomics data > > > +formats when enabled.=C2=A0 Parallel decompression is somewhat faste= r, > > > but truly the > > =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 > > ^^^^^^^^^^^^^ > > > +speedup comes during compression.") > > =C2=A0=C2=A0 ^^^^^^^ > >=20 > > =E2=80=9Cbut the true speedup=E2=80=9D instead? >=20 > Sure. I usually don't change descriptions as given by the creators of > the software, but I applied your suggestion. >=20 > Thank you for the elaborate suggestions! >=20 > I attached another version of the patch, which I hope is fine now. :) >=20 > Kind regards, > Roel Janssen >=20 >=20 > From 1af29f66980ba19740e05a27135f141e23b7fd3f Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Fri, 30 Apr 2021 13:47:43 +0200 > Subject: [PATCH] gnu: Add pbgzip. >=20 > * gnu/packages/bioinformatics.scm (pbgzip): New variable. > --- > gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++- > 1 file changed, 35 insertions(+), 1 deletion(-) >=20 > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm > index 83ebfc2d8f..cd2dae05d5 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -3,7 +3,7 @@ > ;;; Copyright =C2=A9 2015, 2016, 2017, 2018 Ben Woodcroft > ;;; Copyright =C2=A9 2015, 2016, 2018, 2019, 2020 Pjotr Prins > ;;; Copyright =C2=A9 2015 Andreas Enge > -;;; Copyright =C2=A9 2016, 2020 Roel Janssen > +;;; Copyright =C2=A9 2016, 2020, 2021 Roel Janssen > ;;; Copyright =C2=A9 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner = > ;;; Copyright =C2=A9 2016, 2020 Marius Bakke > ;;; Copyright =C2=A9 2016, 2018 Raoul Bonnal > @@ -571,6 +571,40 @@ input and output BAMs must adhere to the PacBio BAM = format specification. > Non-PacBio BAMs will cause exceptions to be thrown.") > (license license:bsd-3))) > =20 > +(define-public pbgzip > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) > + (package > + (name "pbgzip") > + (version (git-version "0.0.0" "0" commit)) > + (source (origin > + (method git-fetch) > + (uri (git-reference > + (url "https://github.com/nh13/pbgzip") > + (commit commit))) > + (file-name (git-file-name name version)) > + (sha256 > + (base32 > + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"= )))) > + (build-system gnu-build-system) > + (native-inputs > + `(("autoconf" ,autoconf) > + ("automake" ,automake))) > + (inputs > + `(("zlib" ,zlib))) > + (home-page "https://github.com/nh13/pbgzip") > + (synopsis "Parallel Block GZIP") > + (description "This package implements parallel block gzip. For ma= ny > +formats, in particular genomics data formats, data are compressed in I wasn't sure about 'data are' vs 'data is' but I think data here is plural, so 'data are' should be right. > +fixed-length blocks such that they can be easily indexed based on a (gen= omic) > +coordinate order, since typically each block is sorted according to this= order. > +This allows for each block to be individually compressed (deflated), or = more > +importantly, decompressed (inflated), with the latter enabling random re= trieval > +of data in large files (gigabytes to terabytes). @code{pbgzip} is not l= imited > +to any particular format, but certain features are tailored to genomics = data > +formats when enabled. Parallel decompression is somewhat faster, but th= e true > +speedup comes during compression.") > + (license license:expat)))) > + > (define-public blasr-libcpp > (package > (name "blasr-libcpp") > --=20 > 2.31.1 >=20 Looks good 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 --saCnEgrzqfQvnK7S Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAmCL78UACgkQQarn3Mo9 g1HyzQ//fuPkFgnSuU0kom2qkiA6m+R8a4ilzGRv+dgYc2XIaEZ0mZt4Pcg8Hj6B 6wIuiIs+aFjJZ6jaobnhS62B9D7hb5+v6Gy5GPk9fm8XGQjHMwlDWxvTLSc06LD8 cjYMjHH8INeaTaB9ne2AOgDf1l90mOfaYG2RWs6k4TpEwwER8erqGN3sf8Xa9ikl 6Ki/ygivAw/TEhJaFL4KPaVkLNh2HSlH0gjW1HLJgTWwe2gjSg/RVWnHFel1sY0a dzt5OeuUSLEg0zZzy9zQKUOvB/pldWJl7j1sOlSkSe2OwaLGASvX5UU+zA2v72gZ fTOhAOCytfd6EbhoIc/6i4M3GUb+/q1hUfYXq4B0HxvCQYMfyF8nRXeu130d9bcF 8HiYdIAkhTXL+Ld1CoQogIlMriJEnS37mdBxR5uqdn5g+AillUDhejFMCKhOSRqv PSXUd1cm/uySWlBAzumG9+eqLIYXNVt0yz2ksrjkqJC3S5jQN0Q79tB3P4qTe35b uvy4Ug/crxfD7sCJ7KtjWbZeKsuwUV7yHs/2Xg9/HmArvN99nM3XJftNYGcX9YY2 P8Ykfc2pmSG3DYWR0l8hSPuz8ZZiEIXNy5jWxa7TeGTvi+e2sGqWz6ahfPRQrrIt cn/t3VFnCa9+v00XklHI+FGOYaPef97ztmO+o4cApdFHD6UFiZ4= =RtpN -----END PGP SIGNATURE----- --saCnEgrzqfQvnK7S-- From unknown Sat Jun 21 05:17:06 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Roel Janssen Subject: bug#47930: closed (Re: [bug#47930] [PATCH] gnu: Add pbgzip.) Message-ID: References: <288c615cc9a12c6333a28f7002429140c2924ae5.camel@gnu.org> X-Gnu-PR-Message: they-closed 47930 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 47930@debbugs.gnu.org Date: Fri, 30 Apr 2021 16:49:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1619801342-8600-1" This is a multi-part message in MIME format... ------------=_1619801342-8600-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #47930: [PATCH] gnu: Add pbgzip. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 47930@debbugs.gnu.org. --=20 47930: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D47930 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1619801342-8600-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 47930-done) by debbugs.gnu.org; 30 Apr 2021 16:48:12 +0000 Received: from localhost ([127.0.0.1]:59721 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lcWJH-0002DR-Ji for submit@debbugs.gnu.org; Fri, 30 Apr 2021 12:48:11 -0400 Received: from eggs.gnu.org ([209.51.188.92]:54586) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lcWJF-0002DC-3q for 47930-done@debbugs.gnu.org; Fri, 30 Apr 2021 12:48:09 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:52081) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lcWJ8-0000lc-BH; Fri, 30 Apr 2021 12:48:02 -0400 Received: from 2001-1c02-0b18-2900-222e-248e-9586-e52d.cable.dynamic.v6.ziggo.nl ([2001:1c02:b18:2900:222e:248e:9586:e52d]:50110) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1lcWJ7-0006gj-Kc; Fri, 30 Apr 2021 12:48:02 -0400 Message-ID: <288c615cc9a12c6333a28f7002429140c2924ae5.camel@gnu.org> Subject: Re: [bug#47930] [PATCH] gnu: Add pbgzip. From: Roel Janssen To: Efraim Flashner Date: Fri, 30 Apr 2021 18:47:59 +0200 In-Reply-To: References: <874kfz71ni.fsf@yoctocell.xyz> <87czucnphi.fsf@yoctocell.xyz> <052ee880cea08e4e1627a2181f7173ab9587b6c8.camel@gnu.org> Content-Type: text/plain; charset="UTF-8" User-Agent: Evolution 3.40.0 (3.40.0-1.fc34) MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 47930-done Cc: Xinglu Chen , 47930-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 Fri, 2021-04-30 at 14:53 +0300, Efraim Flashner wrote: > > > > From 1af29f66980ba19740e05a27135f141e23b7fd3f Mon Sep 17 00:00:00 > > 2001 > > From: Roel Janssen > > Date: Fri, 30 Apr 2021 13:47:43 +0200 > > Subject: [PATCH] gnu: Add pbgzip. > > > > ... > > +      (synopsis "Parallel Block GZIP") > > +      (description "This package implements parallel block gzip.  > > For many > > +formats, in particular genomics data formats, data are compressed > > in > > I wasn't sure about 'data are' vs 'data is' but I think data here is > plural, so 'data are' should be right. > > > +fixed-length blocks such that they can be easily indexed based on > > a (genomic) > > +coordinate order, since typically each block is sorted according > > to this order. > > +This allows for each block to be individually compressed > > (deflated), or more > > +importantly, decompressed (inflated), with the latter enabling > > random retrieval > > +of data in large files (gigabytes to terabytes).  @code{pbgzip} is > > not limited > > +to any particular format, but certain features are tailored to > > genomics data > > +formats when enabled.  Parallel decompression is somewhat faster, > > but the true > > +speedup comes during compression.") > > +      (license license:expat)))) > > + > >  (define-public blasr-libcpp > >    (package > >      (name "blasr-libcpp") > > -- > > 2.31.1 > > > > Looks good to me! > Thank you Efraim, and thank you Xinglu Chen. I pushed this patch. Kind regards, Roel Janssen ------------=_1619801342-8600-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 21 Apr 2021 12:27:14 +0000 Received: from localhost ([127.0.0.1]:57131 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lZBwi-0005i1-Hk for submit@debbugs.gnu.org; Wed, 21 Apr 2021 08:27:14 -0400 Received: from lists.gnu.org ([209.51.188.17]:47738) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lZBwe-0005hr-S9 for submit@debbugs.gnu.org; Wed, 21 Apr 2021 08:27:07 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:49874) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lZBwd-0004le-5t for guix-patches@gnu.org; Wed, 21 Apr 2021 08:27:03 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:54810) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lZBwc-0001On-Kw for guix-patches@gnu.org; Wed, 21 Apr 2021 08:27:02 -0400 Received: from [143.121.198.253] (port=57430) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1lZBwX-0004Gt-8f for guix-patches@gnu.org; Wed, 21 Apr 2021 08:27:00 -0400 To: guix-patches@gnu.org From: Roel Janssen Subject: [PATCH] gnu: Add pbgzip. Message-ID: Date: Wed, 21 Apr 2021 14:26:47 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.7.1 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="------------307951D33DB4D2430D3BCAC4" Content-Language: en-US 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: -1.0 (-) This is a multi-part message in MIME format. --------------307951D33DB4D2430D3BCAC4 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi Guix, Here's a patch to add pbgzip.  Lint complains that there is no release on the Github page, but there's nothing I can do about it. Kind regards, Roel Janssen --------------307951D33DB4D2430D3BCAC4 Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-Add-pbgzip.patch" Content-Transfer-Encoding: 8bit Content-Disposition: attachment; filename="0001-gnu-Add-pbgzip.patch" >From 3d34e82ee67f5ee0b226de350f40d7f881169a56 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 21 Apr 2021 14:24:07 +0200 Subject: [PATCH] gnu: Add pbgzip. * gnu/packages/bioinformatics.scm (pbgzip): New variable. --- gnu/packages/bioinformatics.scm | 42 ++++++++++++++++++++++++++++++++- 1 file changed, 41 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 31205c473a..35601378c2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins ;;; Copyright © 2015 Andreas Enge -;;; Copyright © 2016, 2020 Roel Janssen +;;; Copyright © 2016, 2020, 2021 Roel Janssen ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner ;;; Copyright © 2016, 2020 Marius Bakke ;;; Copyright © 2016, 2018 Raoul Bonnal @@ -569,6 +569,46 @@ input and output BAMs must adhere to the PacBio BAM format specification. Non-PacBio BAMs will cause exceptions to be thrown.") (license license:bsd-3))) +(define-public pbgzip + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974")) + (package + (name "pbgzip") + (version (string-take commit 7)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nh13/pbgzip") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'autogen + (lambda _ + (zero? (system* "sh" "autogen.sh"))))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/nh13/pbgzip") + (synopsis "Parallel Block GZIP") + (description "This package implements parallel block gzip. For many +formats, in particular genomics data formats, data are compressed in +fixed-length blocks such that they can be easily indexed based on a (genomic) +coordinate order, since typically each block is sorted according to this order. +This allows for each block to be individually compressed (deflated), or more +importantly, decompressed (inflated), with the latter enabling random retrieval +of data in large files (gigabytes to terabytes). @code{pbgzip} is not limited +to any particular format, but certain features are tailored to genomics data +formats when enabled. Parallel decompression is somewhat faster, but truly the +speedup comes during compression.") + (license license:expat)))) + (define-public blasr-libcpp (package (name "blasr-libcpp") -- 2.31.1 --------------307951D33DB4D2430D3BCAC4-- ------------=_1619801342-8600-1--