From e24f4de21ee3c367c38e431626f4796795eb9e18 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Wed, 17 Jun 2015 11:49:27 +1000
Subject: [PATCH] gnu: Add diamond.

* gnu/packages/bioinformatics.scm (diamond): New variable.
---
 gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0d8a6d5..94db812 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -28,6 +28,7 @@
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
+  #:use-module (gnu packages algebra)
   #:use-module (gnu packages base)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
@@ -615,6 +616,51 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
 other types of unwanted sequence from high-throughput sequencing reads.")
     (license license:expat)))
 
+(define-public diamond
+  (package
+    (name "diamond")
+    (version "0.7.9")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append
+                "https://github.com/bbuchfink/diamond/archive/v" version ".tar.gz"))
+              (sha256
+               (base32
+                "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f ;no "check" target
+		#:phases
+		(alist-cons-after
+		 'unpack 'enter-source-dir
+		 (lambda _ (chdir "src"))
+		 (alist-replace
+		  'install
+		  (lambda* (#:key outputs #:allow-other-keys)
+			   (let ((bin (string-append
+				       (assoc-ref outputs "out") "/bin")))
+			     (mkdir-p bin)
+			     (copy-file "../bin/diamond" (string-append bin "/diamond"))))
+		  (alist-delete 'configure %standard-phases)))))
+    (native-inputs
+     `(("bc" ,bc)))
+    (inputs
+     `(("boost" ,boost)
+       ("zlib" ,zlib)))
+    (home-page "https://github.com/bbuchfink/diamond")
+    (synopsis "Accelerated BLAST compatible local sequence aligner")
+    (description
+     "DIAMOND is a BLAST-compatible local aligner for mapping protein and
+translated DNA query sequences against a protein reference database (BLASTP
+and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
+reads at a typical sensitivity of 90-99% relative to BLAST depending on the
+data and settings.")
+    (license (license:non-copyleft (string-append "https://github.com/bbuchfink"
+						  "/diamond/blob/v"
+						  version
+						  "/src/COPYING")))))
+
 (define-public edirect
   (package
     (name "edirect")
-- 
2.1.4