From: Roel Janssen <roel@gnu.org>
To: Xinglu Chen <public@yoctocell.xyz>,
Efraim Flashner <efraim@flashner.co.il>,
Maxime Devos <maximedevos@telenet.be>
Cc: 47930@debbugs.gnu.org
Subject: [bug#47930] [PATCH] gnu: Add pbgzip.
Date: Fri, 30 Apr 2021 13:48:48 +0200 [thread overview]
Message-ID: <052ee880cea08e4e1627a2181f7173ab9587b6c8.camel@gnu.org> (raw)
In-Reply-To: <87czucnphi.fsf@yoctocell.xyz>
[-- Attachment #1: Type: text/plain, Size: 2632 bytes --]
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!
I attached another version of the patch, which I hope is fine now. :)
Kind regards,
Roel Janssen
[-- Attachment #2: 0001-gnu-Add-pbgzip.patch --]
[-- Type: text/x-patch, Size: 2991 bytes --]
From 1af29f66980ba19740e05a27135f141e23b7fd3f Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 30 Apr 2021 13:47:43 +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..cd2dae05d5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3,7 +3,7 @@
;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
@@ -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 (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 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 the true
+speedup comes during compression.")
+ (license license:expat))))
+
(define-public blasr-libcpp
(package
(name "blasr-libcpp")
--
2.31.1
next prev parent reply other threads:[~2021-04-30 13:33 UTC|newest]
Thread overview: 10+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-04-21 12:26 [bug#47930] [PATCH] gnu: Add pbgzip Roel Janssen
2021-04-21 21:44 ` Xinglu Chen
2021-04-21 21:45 ` Xinglu Chen
2021-04-22 16:40 ` Maxime Devos
2021-04-29 7:29 ` Efraim Flashner
2021-04-29 12:22 ` Roel Janssen
2021-04-30 8:30 ` Xinglu Chen
2021-04-30 11:48 ` Roel Janssen [this message]
2021-04-30 11:53 ` Efraim Flashner
2021-04-30 16:47 ` bug#47930: " Roel Janssen
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