From afeb10a056e1f5f2c492ace9ee0a33f09cb53e8a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 6 Mar 2019 15:25:37 +0100
Subject: gnu: Add bowtie1.

* gnu/packages/bioinformatics.scm (bowtie1): New variable.
---
 gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 092c49d8cb..4b775d8b7d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1384,6 +1384,46 @@ gapped, local, and paired-end alignment modes.")
     (supported-systems '("x86_64-linux"))
     (license license:gpl3+)))
 
+(define-public bowtie1
+  (package
+    (name "bowtie1")
+    (version "1.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/"
+                                  version "/bowtie-" version "-src.zip"))
+              (sha256
+               (base32
+                "1jl2cj9bz8lwz8dwnxbycn8yp8g4kky62fkcxifyf1ri0y6n2vc0"))
+              (modules '((guix build utils)))
+              (snippet
+               '(substitute* "Makefile"
+                  ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+                  (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+                  (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f                      ; no "check" target
+       #:make-flags
+       (list "all"
+             (string-append "prefix=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))))
+    (inputs
+     `(("tbb" ,tbb)
+       ("zlib" ,zlib)))
+    (supported-systems '("x86_64-linux"))
+    (home-page "http://bowtie-bio.sourceforge.net/index.shtml")
+    (synopsis "Fast aligner for short nucleotide sequence reads")
+    (description
+     "Bowtie is a fast, memory-efficient short read aligner.  It aligns short
+DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
+reads per hour.  Bowtie indexes the genome with a Burrows-Wheeler index to
+keep its memory footprint small: typically about 2.2 GB for the human
+genome (2.9 GB for paired-end).")
+    (license license:artistic2.0)))
+
 (define-public tophat
   (package
     (name "tophat")
-- 
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