From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:8:6d80::]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id yEoXOrGnimAWoAAAgWs5BA (envelope-from ) for ; Thu, 29 Apr 2021 14:33:53 +0200 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id wOgHNrGnimA5BwAA1q6Kng (envelope-from ) for ; Thu, 29 Apr 2021 12:33:53 +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 55731261A1 for ; Thu, 29 Apr 2021 14:33:53 +0200 (CEST) Received: from localhost ([::1]:53510 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lc5rc-0003tf-Hb for larch@yhetil.org; Thu, 29 Apr 2021 08:33:52 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:44312) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lc5i6-0004HZ-Ge for guix-patches@gnu.org; Thu, 29 Apr 2021 08:24:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43479) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lc5i6-0000yq-6v for guix-patches@gnu.org; Thu, 29 Apr 2021 08:24:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lc5i6-00056u-2Y for guix-patches@gnu.org; Thu, 29 Apr 2021 08:24:02 -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: 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-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=1619699633; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:in-reply-to:in-reply-to:references:references: list-id:list-help:list-unsubscribe:list-subscribe:list-post; bh=bVS9LG8C9mX7FEXOK06ceXDd7B5cA2l8hmuHBd+WK7s=; b=j+Ff4035qvQdd9yeZL69hlhz/gvFTk/55Q2PoSwLUIdVXEdXHj2Acd5zLwUGIrnoqmYCUC B7FtAfTwYKiW3xcS6p9Ykvsa1cKjFBjM5YGyZLBhjKa7JXgvfIzZMa+Wc3JhZcn8DZGBni 5ApAHSVNi7A1U/qBNtS5PC2XhQsalYgddwXPS1i6DpL3oaHDLgsHOBGFirlcYHNhLCjetG eJYwyOCUiHeAAeqPWWr1ndV3pbaRfof6rnpn7uEliJTsdGeLKek75irG930dPpTpMu22D1 W1DNdPDcu2tpGJUu5euc6cceBYMqU2pNYsE7N2lGpmKuFSLRF+gycV9OH62/oQ== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1619699633; a=rsa-sha256; cv=none; b=LQcw9u1RWiMA1Ifd72wvfmV58luLZqwvcs3V6SitOQPN5ABB7QzMIiPYy9bXzVkSwfWiwi FNATVq6P8KJd8vgfCqVWCQl8o0IYhep9Mxnpwy9nfxbSwmSfCEPEtz0OFvizvY8LQCVdDE xQuWekbZlEiKkNNxOPWqGHCocH7OZa2AsBFjcFzatN7TOVNio5vTm75xyS0NvuMU2vrguM ltPkxQrvnOZeJb9Z79U9uoa4e7xtufK7btPpLdknYqAif8vA93NJ8lKJmSPxnF9IiTDlBZ rdMq5MOeiRpBRl3UHj1JV1uzfr/7rybQvrB6QuKkZUBri0/0yYyITHuvvFuE9w== ARC-Authentication-Results: i=1; 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-Spam-Score: -3.59 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: 55731261A1 X-Spam-Score: -3.59 X-Migadu-Scanner: scn0.migadu.com X-TUID: Ku2bMRH8dPT6 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--