From: Roel Janssen <roel@gnu.org>
To: 47930@debbugs.gnu.org
Subject: [bug#47930] [PATCH] gnu: Add pbgzip.
Date: Wed, 21 Apr 2021 14:26:47 +0200 [thread overview]
Message-ID: <eb1b7cd3-e60b-46c5-da4a-371b5038b3a3@gnu.org> (raw)
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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
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From 3d34e82ee67f5ee0b226de350f40d7f881169a56 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
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 <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>
@@ -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
next reply other threads:[~2021-04-21 12:42 UTC|newest]
Thread overview: 10+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-04-21 12:26 Roel Janssen [this message]
2021-04-21 21:44 ` [bug#47930] [PATCH] gnu: Add pbgzip 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
2021-04-30 11:53 ` Efraim Flashner
2021-04-30 16:47 ` bug#47930: " Roel Janssen
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