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