[PATCH] gnu: Add freebayes

[Rob Syme <rob.syme@gmail.com>]

A guix-friendly licensed variant caller.

From 78fb1be26ca1a0ac768ce5b98f7fd9f467870b84 Mon Sep 17 00:00:00 2001
From: Rob Syme <rob.syme@gmail.com>
Date: Mon, 2 May 2016 16:46:53 +0800
Subject: [PATCH] gnu: Add freebayes

* gnu/packages/bioinformatics.scm (freebayes): New variable.

---
 gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 079fd46..db382d7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -43,6 +43,7 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpio)
+  #:use-module (gnu packages cmake)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages doxygen)
   #:use-module (gnu packages datastructures)
@@ -1905,6 +1906,44 @@ genes in incomplete assemblies or complete genomes.")
     ;; GPL3+ according to private correspondense with the authors.
     (license license:gpl3+)))

+(define-public freebayes
+  (let ((commit "0cb269728b2db6307053cafe6f913a8b6fa1331e"))
+    (package
+      (name "freebayes")
+      (version "1.0.2")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ekg/freebayes.git")
+                      (commit commit)
+                      (recursive? #t)))
+                (sha256
+                 (base32
+                  "0z37ch3as3g8hx36l1lwy1v9cqahx72lb51yxrcmwymx0kcf39c5"))))
+      (build-system gnu-build-system)
+      (arguments '(#:phases
+                   (modify-phases %standard-phases
+                     (delete 'configure)
+                     (delete 'check) ; no "check" target
+                     (replace 'install
+                       (lambda* (#:key outputs #:allow-other-keys)
+                         (let* ((out (assoc-ref outputs "out"))
+                                (bin (string-append out "/bin")))
+                           (install-file "bin/freebayes" bin)
+                           (install-file "bin/bamleftalign" bin)
+                           #t))))))
+      (inputs
+       `(("cmake" ,cmake)
+         ("zlib" ,zlib)))
+      (home-page "https://github.com/ekg/freebayes")
+      (synopsis "Bayesian haplotype-based polymorphism discovery and
genotyping")
+      (description "FreeBayes is a Bayesian genetic variant detector
designed to
+find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
+indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
+complex events (composite insertion and substitution events) smaller than the
+length of a short-read sequencing alignment.")
+      (license license:expat))))
+
 (define-public fxtract
   (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
     (package
-- 
2.7.4