>From 7e0352fad776f1c491882647ee3ad5f5319e1164 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
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
