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02/02: gnu: Add flexbar.
From: |
Ricardo Wurmus |
Subject: |
02/02: gnu: Add flexbar. |
Date: |
Mon, 09 Feb 2015 09:26:46 +0000 |
rekado pushed a commit to branch master
in repository guix.
commit d7678942f9a4a4f046e0781ab89ce62680ded24c
Author: Ricardo Wurmus <address@hidden>
Date: Fri Feb 6 15:42:02 2015 +0100
gnu: Add flexbar.
* gnu/packages/bioinformatics.scm (flexbar): New variable.
---
gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++++++
1 files changed, 42 insertions(+), 0 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0cae827..c0d1438 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21,6 +21,7 @@
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system cmake)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gnu packages base)
@@ -29,6 +30,7 @@
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python))
+ #:use-module (gnu packages tbb)
(define-public bedtools
(package
@@ -139,6 +141,46 @@ gapped, local, and paired-end alignment modes.")
(supported-systems '("x86_64-linux"))
(license license:gpl3+)))
+(define-public flexbar
+ (package
+ (name "flexbar")
+ (version "2.5")
+ (source (origin
+ (method url-fetch)
+ (uri
+ (string-append "mirror://sourceforge/flexbar/"
+ version "/flexbar_v" version "_src.tgz"))
+ (sha256
+ (base32
+ "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(;; There is no test target, although there is a directory containing
+ ;; test data and scripts (launched by flexbar_validate.sh).
+ #:tests? #f
+ #:configure-flags (list
+ (string-append "-DFLEXBAR_BINARY_DIR="
+ (assoc-ref %outputs "out")
+ "/bin/"))
+ #:phases
+ (alist-delete 'install %standard-phases)))
+ (inputs
+ `(("tbb" ,tbb)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)
+ ("seqan" ,seqan)))
+ (home-page "http://flexbar.sourceforge.net")
+ (synopsis "Barcode and adapter removal tool for sequencing platforms")
+ (description
+ "Flexbar preprocesses high-throughput nucleotide sequencing data
+efficiently. It demultiplexes barcoded runs and removes adapter sequences.
+Moreover, trimming and filtering features are provided. Flexbar increases
+read mapping rates and improves genome and transcriptome assemblies. It
+supports next-generation sequencing data in fasta/q and csfasta/q format from
+Illumina, Roche 454, and the SOLiD platform.")
+ (license license:gpl3)))
+
(define-public samtools
(package
(name "samtools")