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branch master updated: gnu: Add pbgzip.
From: |
guix-commits |
Subject: |
branch master updated: gnu: Add pbgzip. |
Date: |
Fri, 30 Apr 2021 12:45:19 -0400 |
This is an automated email from the git hooks/post-receive script.
roelj pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new f09e4dd gnu: Add pbgzip.
f09e4dd is described below
commit f09e4dd8ea6b86ecbae9c90e0316f6fa44b546d6
Author: Roel Janssen <roel@gnu.org>
AuthorDate: Fri Apr 30 13:47:43 2021 +0200
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 83ebfc2..cd2dae0 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")
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