From patchwork Wed Apr 21 12:26:47 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Roel Janssen X-Patchwork-Id: 28727 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 B28B827BC7A; Wed, 21 Apr 2021 13:42:33 +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,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 4DFE727BC79 for ; Wed, 21 Apr 2021 13:42:30 +0100 (BST) Received: from localhost ([::1]:49034 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lZCBZ-0001Hl-HL for patchwork@mira.cbaines.net; Wed, 21 Apr 2021 08:42:29 -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-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+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches 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 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