* [PATCH]: gnu: Add flexbar.
@ 2015-02-06 14:43 Ricardo Wurmus
2015-02-07 22:48 ` Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2015-02-06 14:43 UTC (permalink / raw)
To: guix-devel
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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
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH]: gnu: Add flexbar.
2015-02-06 14:43 [PATCH]: gnu: Add flexbar Ricardo Wurmus
@ 2015-02-07 22:48 ` Ludovic Courtès
0 siblings, 0 replies; 2+ messages in thread
From: Ludovic Courtès @ 2015-02-07 22:48 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
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’.
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2015-02-06 14:43 [PATCH]: gnu: Add flexbar Ricardo Wurmus
2015-02-07 22:48 ` Ludovic Courtès
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