>From 713bb1145ff901c4069f2fadb210d8eb842981da Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Tue, 16 Dec 2014 17:52:44 +0100
Subject: [PATCH] gnu: Add bowtie

* gnu/packages/bioinformatics.scm (bowtie): New variable.
---
 gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6f6178a..755287d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -28,6 +28,66 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python))
 
+(define-public bowtie
+  (package
+    (name "bowtie")
+    (version "2.2.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))))
+    (build-system gnu-build-system)
+    (inputs `(("perl" ,perl)
+              ("perl-clone" ,perl-clone)
+              ("perl-test-deep" ,perl-test-deep)
+              ("perl-test-simple" ,perl-test-simple)
+              ("python" ,python-2)))
+    (arguments
+     '(#:make-flags '("allall")
+       #:phases
+       (alist-cons-after
+        'unpack
+        'patch-makefile
+        (lambda _
+          (substitute* "Makefile"
+            (("^CC = .*$") (string-append "CC = " (which "gcc")))
+            (("^CPP = .*$") (string-append "CPP = " (which "g++")))
+            ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+            (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+            (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
+        (alist-delete
+         'configure
+         (alist-replace
+          'install
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+              (mkdir-p bin)
+              (for-each (lambda (file)
+                          (copy-file file (string-append bin file)))
+                        (find-files "." "bowtie2.*"))))
+          (alist-replace
+           'check
+           (lambda* (#:key outputs #:allow-other-keys)
+             (system* "perl"
+                      "scripts/test/simple_tests.pl"
+                      "--bowtie2=./bowtie2"
+                      "--bowtie2-build=./bowtie2-build"))
+           %standard-phases))))))
+    (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
+    (synopsis "Fast and sensitive nucleotide sequence read aligner")
+    (description
+     "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
+reads to long reference sequences.  It is particularly good at aligning reads
+of about 50 up to 100s or 1,000s of characters, and particularly good at
+aligning to relatively long (e.g. mammalian) genomes.  Bowtie 2 indexes the
+genome with an FM Index to keep its memory footprint small: for the human
+genome, its memory footprint is typically around 3.2 GB.  Bowtie 2 supports
+gapped, local, and paired-end alignment modes.")
+    (license license:gpl3)))
+
 (define-public samtools
   (package
     (name "samtools")
-- 
1.9.3