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spf=pass (aspmx2.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 2.72 Authentication-Results: aspmx2.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=s14W27df; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx2.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 9F9ED147A1 X-Spam-Score: 2.72 X-Migadu-Scanner: scn0.migadu.com X-TUID: qY2BxzVsRMPs * gnu/packages/bioinformatics.scm (r-shortread): Move from here... * gnu/packages/bioconductor.scm (r-shortread): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 --------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f4088db27..05077b422e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1845,6 +1845,49 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-shortread + (package + (name "r-shortread") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ShortRead" version)) + (sha256 + (base32 + "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) + (properties `((upstream-name . "ShortRead"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-rhtslib" ,r-rhtslib) + ("r-hwriter" ,r-hwriter) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/ShortRead") + (synopsis "FASTQ input and manipulation tools") + (description + "This package implements sampling, iteration, and input of FASTQ files. +It includes functions for filtering and trimming reads, and for generating a +quality assessment report. Data are represented as +@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of +purposes. The package also contains legacy support for early single-end, +ungapped alignment formats.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 186b051865..fda4516052 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,49 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-shortread - (package - (name "r-shortread") - (version "1.48.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ShortRead" version)) - (sha256 - (base32 - "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) - (properties `((upstream-name . "ShortRead"))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/ShortRead") - (synopsis "FASTQ input and manipulation tools") - (description - "This package implements sampling, iteration, and input of FASTQ files. -It includes functions for filtering and trimming reads, and for generating a -quality assessment report. Data are represented as -@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of -purposes. The package also contains legacy support for early single-end, -ungapped alignment formats.") - (license license:artistic2.0))) - (define-public r-systempiper (package (name "r-systempiper") -- 2.30.1