diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 35 |
1 files changed, 34 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e143fb2c55..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") @@ -871,7 +904,7 @@ generated using the PacBio Iso-Seq protocol.") (string-append "mirror://sourceforge/rseqc/" version "/RSeQC-" version ".tar.gz")) (sha256 - (base32 "09rf0x9d6apjja5l01cgprj7vigpw6kiqhy34ibwwlxil0db0ri4")) + (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330")) (modules '((guix build utils))) (snippet '(begin |