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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-02-06 15:42:02 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-02-09 10:26:28 +0100 |
| commit | d7678942f9a4a4f046e0781ab89ce62680ded24c (patch) | |
| tree | f047f4df1ca2db1c7b8559f5cb438b2055d2d978 /gnu | |
| parent | d3517eda25c74758ddedb04fa781aa65549248fe (diff) | |
| download | patches-d7678942f9a4a4f046e0781ab89ce62680ded24c.tar patches-d7678942f9a4a4f046e0781ab89ce62680ded24c.tar.gz | |
gnu: Add flexbar.
* gnu/packages/bioinformatics.scm (flexbar): New variable.
Diffstat (limited to 'gnu')
| -rw-r--r-- | 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 0cae8274d5..c0d14388e1 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") |