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Change-Id: Ib74974b0ee887753d6ead5b5b388e7163abb11f8 --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) base-commit: 1f26b0eec83b5dc949900a743ed01088cb093c65 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f7f39f525d..0129b9ebeb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14542,6 +14542,40 @@ (define-public shorah frequency of the different genetic variants present in a mixed sample.") (license license:gpl3+))) +(define-public sickle + (package + (name "sickle") + (version "1.33") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/najoshi/sickle") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1bnq480lpylq9sfsa1y71b4qz0ipi2zjnp8ds48fh10ijlwmwmdc")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ;There are no tests + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (install-file "sickle" + (string-append #$output "/bin"))))))) + (propagated-inputs (list zlib)) + (home-page "https://github.com/najoshi/sickle") + (synopsis "Adaptive trimming tool for FASTQ files using quality") + (description + "Sickle is a tool that trims reads based on quality and length thresholds. +It uses sliding windows to detect low-quality bases at the 3'-end and +high-quality bases at the 5'-end. Additionally, it discards reads based +on the length threshold.") + (license license:expat))) + (define-public ruby-bio-kseq (package (name "ruby-bio-kseq")