[PATCH]: gnu: Add flexbar.

[PATCH]: gnu: Add flexbar.

[Ricardo Wurmus]

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Hi Guix,

attached is a patch to add another common bioinformatics tool to the
bioinformatics module: flexbar.

~~ Ricardo


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From fc082d741f31fb6260c8fd92332d63ed40e592e5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 6 Feb 2015 15:42:02 +0100
Subject: [PATCH] gnu: Add flexbar.

* gnu/packages/bioinformatics.scm (flexbar): New variable.
---
 gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 54c1a82..586abec 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")
-- 
2.1.0

Re: [PATCH]: gnu: Add flexbar.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From fc082d741f31fb6260c8fd92332d63ed40e592e5 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 6 Feb 2015 15:42:02 +0100
> Subject: [PATCH] gnu: Add flexbar.
>
> * gnu/packages/bioinformatics.scm (flexbar): New variable.

LGTM, thanks.

Ludo’.