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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-04-14 16:36:30 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-04-16 10:28:37 +0200 |
| commit | 2127cedb23ab051d9f03bdab7b7ae5d5c472baff (patch) | |
| tree | 49d97d20d56dc13760fb828d5192ae9bc54b0879 | |
| parent | f571e1c34600dc4621506e8745e36442f9896970 (diff) | |
| download | patches-2127cedb23ab051d9f03bdab7b7ae5d5c472baff.tar patches-2127cedb23ab051d9f03bdab7b7ae5d5c472baff.tar.gz | |
gnu: Add FASTX Toolkit.
* gnu/packages/bioinformatics.scm (fastx-toolkit): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 33 |
1 files changed, 33 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1ad5f600fb..b1258220b4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -39,6 +39,7 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages swig) #:use-module (gnu packages tbb) + #:use-module (gnu packages textutils) #:use-module (gnu packages vim) #:use-module (gnu packages xml) #:use-module (gnu packages zip)) @@ -471,6 +472,38 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") other types of unwanted sequence from high-throughput sequencing reads.") (license license:expat))) +(define-public fastx-toolkit + (package + (name "fastx-toolkit") + (version "0.0.14") + (source (origin + (method url-fetch) + (uri + (string-append + "https://github.com/agordon/fastx_toolkit/releases/download/" + version "/fastx_toolkit-" version ".tar.bz2")) + (sha256 + (base32 + "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy")))) + (build-system gnu-build-system) + (inputs + `(("libgtextutils" ,libgtextutils))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") + (synopsis "Tools for FASTA/FASTQ file preprocessing") + (description + "The FASTX-Toolkit is a collection of command line tools for Short-Reads +FASTA/FASTQ files preprocessing. + +Next-Generation sequencing machines usually produce FASTA or FASTQ files, +containing multiple short-reads sequences. The main processing of such +FASTA/FASTQ files is mapping the sequences to reference genomes. However, it +is sometimes more productive to preprocess the files before mapping the +sequences to the genome---manipulating the sequences to produce better mapping +results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") + (license license:agpl3+))) + (define-public flexbar (package (name "flexbar") |