From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:4a6f::]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id QKqXHrcdgGDlPAEAgWs5BA (envelope-from ) for ; Wed, 21 Apr 2021 14:42:31 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id QOwnGrcdgGBTZAAAbx9fmQ (envelope-from ) for ; Wed, 21 Apr 2021 12:42:31 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 2DA2914A72 for ; Wed, 21 Apr 2021 14:42:31 +0200 (CEST) Received: from localhost ([::1]:49034 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lZCBa-0001Hl-BT for larch@yhetil.org; Wed, 21 Apr 2021 08:42:30 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:50082) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lZBxa-0005ti-WB for guix-patches@gnu.org; Wed, 21 Apr 2021 08:28:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:45585) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lZBxa-0001vS-NI for guix-patches@gnu.org; Wed, 21 Apr 2021 08:28:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lZBxa-0005jG-Ji for guix-patches@gnu.org; Wed, 21 Apr 2021 08:28:02 -0400 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-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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1619008951; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:list-id:list-help:list-unsubscribe:list-subscribe: list-post; bh=qS44c5Z9fa3VSgNqxj9M8t78IsgxP8NjxNNpbo8R6Gw=; b=oZ7b8Qto2tlcqwYlpJuO71nwijzZr7Rw+ZHTU7VIVMKRkCZAVWU3B90YxQP+05c3wlvjV6 ydwTjT14vBlMRTb15DX13xohM08reJUqkN6/d6JNOzVEvg0z3crGgeCOz9lSy0FP/IUKGv Jh5Lf1NVdggtbgleV+2oLOzqZZglgaJdJLhMi6dihNRfhluYeJVqJMJfBz8G5nLIXq9vXZ hlGgTVTTV2w8rTvka9ycXXHhcxXkbY4OMITWnmXHymr/srPgMFoMOJ7pGggbBcCWzv/6py W1brChnmEou67BikI192u1+LgYFfss0tnwVRTNem9GkguWp5+IqPVvUgPEYD3A== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1619008951; a=rsa-sha256; cv=none; b=nkedCocza79PWqMq2GEuK23Uu2qjyU/dYSVf7EB4yzXU6h01ImQ1XgsvDjf5KWcZoGZ/fN 8NZiE9XvjeDUZxMevbtjRXg/aZKhm3gdEQj3P2MSvw95thWNkG08jW2OcXnHqZsvB1Rc89 fmsegXsuk4FEucHjeVeAd+uxLyBXXSW37TOFHPnvh1xHrUkILRH1YXI2GChgYEy911EBBN VsxuqfPL4/V46m2rlatr55HQ9czvGvAX3FJOVuO3Wb+xj7bzwTvctIth2cGTDAP74u5klu zeHwAWESOxgYk+RjdgMt9ReCrDCeNmgzDiWRrkEB6sGqIvpwYM7pea5f2LdmNQ== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: -2.94 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 2DA2914A72 X-Spam-Score: -2.94 X-Migadu-Scanner: scn0.migadu.com X-TUID: df9ItiNQfDTE 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--