>From 6e4a02b441ecfc5cbedfdcd7f8823204ac1a747c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Mon, 29 Feb 2016 15:13:12 +0100
Subject: [PATCH 1/2] gnu: Add gdsl.
* gnu/packages/datastructures.scm (gdsl): New variable.
---
gnu/packages/datastructures.scm | 25 ++++++++++++++++++++++++-
1 file changed, 24 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/datastructures.scm b/gnu/packages/datastructures.scm
index 3614900..74b9fff 100644
--- a/gnu/packages/datastructures.scm
+++ b/gnu/packages/datastructures.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015 Ricardo Wurmus <rek...@elephly.net>
+;;; Copyright © 2015, 2016 Ricardo Wurmus <rek...@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -23,6 +23,29 @@
#:use-module (guix download)
#:use-module (guix build-system gnu))
+(define-public gdsl
+ (package
+ (name "gdsl")
+ (version "1.8")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://download.gna.org/gdsl/";
+ "gdsl-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1v64jvlnj8jfpphphgjgb36p0kv50kwfyqncf0y12f16v8ydyiaw"))))
+ (build-system gnu-build-system)
+ (home-page "http://home.gna.org/gdsl/";)
+ (synopsis "Generic data structures library")
+ (description "The Generic Data Structures Library (GDSL) is a collection
+of routines for generic data structures manipulation. It is a re-entrant
+library fully written from scratch in pure ANSI C. It is designed to offer
+for C programmers common data structures with powerful algorithms, and hidden
+implementation. Available structures are lists, queues, stacks, hash tables,
+binary trees, binary search trees, red-black trees, 2D arrays, permutations
+and heaps.")
+ (license license:gpl2+)))
+
(define-public sparsehash
(package
(name "sparsehash")
--
2.1.0
>From 7208e8b25ff14deac88a133a9c2eb6d5a4ab6a98 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Mon, 29 Feb 2016 15:13:52 +0100
Subject: [PATCH 2/2] gnu: Add bwa-pssm.
* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
---
gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6df7d5c..c81126e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -41,6 +41,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
#:use-module (gnu packages curl)
+ #:use-module (gnu packages datastructures)
#:use-module (gnu packages file)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
@@ -773,6 +774,35 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for
70-100bp Illumina reads.")
(license license:gpl3+)))
+(define-public bwa-pssm
+ (package (inherit bwa)
+ (name "bwa-pssm")
+ (version "0.5.11")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/";
+ "archive/" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("gdsl" ,gdsl)
+ ("zlib" ,zlib)
+ ("perl" ,perl)))
+ (home-page "http://bwa-pssm.binf.ku.dk/";)
+ (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
+ (description
+ "BWA-PSSM is a probabilistic short genomic sequence read aligner based on
+the use of @dfn{position specific scoring matrices} (PSSM). Like many of the
+existing aligners it is fast and sensitive. Unlike most other aligners,
+however, it is also adaptible in the sense that one can direct the alignment
+based on known biases within the data set. It is coded as a modification of
+the original BWA alignment program and shares the genome index structure as
+well as many of the command line options.")
+ (license license:gpl3+)))
+
(define-public python2-bx-python
(package
(name "python2-bx-python")
--
2.1.0
