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 4K3UKf8HjGDFfwEAgWs5BA (envelope-from ) for ; Fri, 30 Apr 2021 15:37:03 +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 qLWLJf8HjGCGGQAA1q6Kng (envelope-from ) for ; Fri, 30 Apr 2021 13:37:03 +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 2A41425493 for ; Fri, 30 Apr 2021 15:37:03 +0200 (CEST) Received: from localhost ([::1]:57800 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lcTKG-0006j7-H6 for larch@yhetil.org; Fri, 30 Apr 2021 09:37:02 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:47224) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lcRib-0001F6-Uk for guix-patches@gnu.org; Fri, 30 Apr 2021 07:54:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:46142) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lcRib-0002IL-LU for guix-patches@gnu.org; Fri, 30 Apr 2021 07:54:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lcRib-0006hk-I7 for guix-patches@gnu.org; Fri, 30 Apr 2021 07:54:01 -0400 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: 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-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=1619789823; 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=syHoiYlOYyJjt/zDeJiuo3/i/r1U5rckxnMYpnnxeY0=; b=p6AO4Z4BHf3y6nENK87q3elXbyttbx1d53kR75xQizjHrBv+UoBSJ0VqgbnQ2y7xCbLakW ukwYAMqSjmK/dRLtScbPENIOvIzrKLSEORJ+da6G+/+KoYjJVpmAPsWYMDzy30e6intn/o fRMvBk2OEQojg3yKnjUqUneC9uZMi9pUtsaA/q/cWVzZ7cPCelUt8FAmwFx9UXQ+PVB1gJ 1OSjqnKhc5YadB5nvAP+QOxUPvqW1kY3j9W/OXgHVqyGggqmJwC5sgnjsgjgUnsiWxxF1F 4/UO02eSY9+19VHmxc3JzcVXEAHGrftDsl/77dgRkaYE/XdPMaUW2TFUGgnOvw== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1619789823; a=rsa-sha256; cv=none; b=jjQ3Zmxnzp49R1C5LcemWePUEMnA1OTV7vtTFZPj2b13LsyjzrcCpdnaqxhonS9djE305D 0GinrcMhrqSkbQ0lV/Qi7YvycEa1d1x1TQs/zOESxoa/yIwg3QsJATCdu0yzjMvbT1zT4F MMRO39E95XCpJI/0AKLqtA8zbmPysf9i2nhiBzRR4ufu0udM21/OQpymHN3WDsYDXN58d4 d0htAr6aJutjHh9zIx2avUZdKYfBy9t4GV8xefKXOt/Y39fFsMyDZM3TKDIzuXkrPoEoRj PCIoIDvdpN+jjKf2Tys+N37x11zb35AhAyFLadhfMawQODt3rp55OYiGFu05/A== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=none; dmarc=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: -4.06 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=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-Queue-Id: 2A41425493 X-Spam-Score: -4.06 X-Migadu-Scanner: scn0.migadu.com X-TUID: tR/Eple5Ac5U --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--