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Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 34 |
1 files changed, 34 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f98f10a2c3..cf2dc57fa7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15232,3 +15232,37 @@ indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.") (license license:expat)))) + +(define-public samblaster + (package + (name "samblaster") + (version "0.1.24") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/GregoryFaust/samblaster.git") + (commit (string-append "v." version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0iv2ddfw8363vb2x8gr3p8g88whb6mb9m0pf71i2cqsbv6jghap7")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (install-file "samblaster" + (string-append (assoc-ref outputs "out") "/bin")) + #t))))) + (home-page "https://github.com/GregoryFaust/samblaster") + (synopsis "Mark duplicates in paired-end SAM files") + (description "Samblaster is a fast and flexible program for marking +duplicates in read-id grouped paired-end SAM files. It can also optionally +output discordant read pairs and/or split read mappings to separate SAM files, +and/or unmapped/clipped reads to a separate FASTQ file. When marking +duplicates, samblaster will require approximately 20MB of memory per 1M read +pairs.") + (license license:expat))) |