[PATCH] Add GDSL and bwa-pssm.

[PATCH] Add GDSL and bwa-pssm.

[Ricardo Wurmus]

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From 6e4a02b441ecfc5cbedfdcd7f8823204ac1a747c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@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 <rekado@elephly.net>
+;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@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


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From 7208e8b25ff14deac88a133a9c2eb6d5a4ab6a98 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@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

Re: [PATCH] Add GDSL and bwa-pssm.

[Leo Famulari]

On Mon, Feb 29, 2016 at 03:14:43PM +0100, Ricardo Wurmus wrote:
> * gnu/packages/datastructures.scm (gdsl): New variable.

Looks good to me.

> * gnu/packages/bioinformatics.scm (bwa-pssm): New variable.

Fascinating package! It looks good to me.

Re: [PATCH] Add GDSL and bwa-pssm.

[Ricardo Wurmus]

Leo Famulari <leo@famulari.name> writes:

> On Mon, Feb 29, 2016 at 03:14:43PM +0100, Ricardo Wurmus wrote:
>> * gnu/packages/datastructures.scm (gdsl): New variable.
>
> Looks good to me.
>
>> * gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
>
> Fascinating package! It looks good to me.

Thanks for the review.  I pushed both.

~~ Ricardo