[PATCH] Add preseq.

[Ricardo Wurmus]

>From 7e0352fad776f1c491882647ee3ad5f5319e1164 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Tue, 23 Jun 2015 10:54:00 +0200
Subject: [PATCH] gnu: Add preseq.

* gnu/packages/bioinformatics.scm (preseq): New variable.
---
 gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 09534a8..3d36120 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2004,6 +2004,57 @@ Databases are stored in a portable image within the file 
system, and can be
 accessed/downloaded on demand across HTTP.")
     (license license:public-domain)))
 
+(define-public preseq
+  (package
+    (name "preseq")
+    (version "1.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append "http://smithlabresearch.org/downloads/preseq-";
+                              version ".tar.bz2"))
+              (sha256
+               (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
+              (modules '((guix build utils)))
+              (snippet
+               ;; Remove bundled samtools.
+               ;; FIXME: Without samtools sources "bam2mr" is not built.
+               '(delete-file-recursively "preseq-master/samtools"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         (add-after
+          'unpack 'enter-dir
+          (lambda _
+            (chdir "preseq-master")
+            #t))
+         (replace 'configure
+                  (lambda* (#:key inputs #:allow-other-keys)
+                    ;; Fix install target
+                    (substitute* "Makefile"
+                      (("\\$\\(ROOT\\)/bin") "$(PREFIX)/bin"))
+                    #t)))
+       #:make-flags (list (string-append "PREFIX="
+                                         (assoc-ref %outputs "out"))
+                          ;; Do not attempt to link samtools objects
+                          "SAMTOOLS_DIR=")))
+    (inputs
+     `(("gsl" ,gsl)
+       ("zlib" ,zlib)))
+    (home-page "http://smithlabresearch.org/software/preseq/";)
+    (synopsis "Program for analyzing library complexity")
+    (description
+     "The preseq package is aimed at predicting and estimating the complexity
+of a genomic sequencing library, equivalent to predicting and estimating the
+number of redundant reads from a given sequencing depth and how many will be
+expected from additional sequencing using an initial sequencing experiment.
+The estimates can then be used to examine the utility of further sequencing,
+optimize the sequencing depth, or to screen multiple libraries to avoid low
+complexity samples.")
+    (license license:gpl3+)))
+
 (define-public sra-tools
   (package
     (name "sra-tools")
-- 
2.1.0