Subject: [PATCH] gnu: Add pbgzip.
From: Roel Janssen <[email-masked]>
To: [email-masked]
Date: Wed, 21 Apr 2021 14:26:47 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

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

From 3d34e82ee67f5ee0b226de350f40d7f881169a56 Mon Sep 17 00:00:00 2001
From: Roel Janssen <[email-masked]>
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 <[email-masked]>
 ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <[email-masked]>
 ;;; Copyright © 2015 Andreas Enge <[email-masked]>
-;;; Copyright © 2016, 2020 Roel Janssen <[email-masked]>
+;;; Copyright © 2016, 2020, 2021 Roel Janssen <[email-masked]>
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <[email-masked]>
 ;;; Copyright © 2016, 2020 Marius Bakke <[email-masked]>
 ;;; Copyright © 2016, 2018 Raoul Bonnal <[email-masked]>
@@ -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