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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48575 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48575@debbugs.gnu.org Cc: zimoun Received: via spool by 48575-submit@debbugs.gnu.org id=B48575.16216288451006 (code B ref 48575); Fri, 21 May 2021 20:28:05 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:25 +0000 Received: from localhost ([127.0.0.1]:37719 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjx-0000G3-0w for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:25 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:41776) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjK-00008e-Em for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:47 -0400 Received: by mail-wm1-f48.google.com with SMTP id l11-20020a05600c4f0bb029017a7cd488f5so5153338wmq.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:46 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=uV9J60wXEm55wLqIR3zB80d1Sl46wMxTOfb2GfAMYO0=; b=O8StaTHkWTaCnqgAADYgb9eKD2mU4Dx/rOMfisSzbwNpWInM52ADpC1Rw/bTp6p6VN mOXzu0Cjr4FyGtlqiCz/j+q0DTrpucChsG3mJrf598fseK3zgd45bomPkRq1HQX2MzRP Y3xkNR4nH9sd4zE+js8XWi4cJLJ8yEA4TUC+J9LQglsiV5EnCGSAUUv4O7evAwZvtF8u kxwBKYcs4ImGoM1yofpSRAMaF0vEShUPSQKQ5F+zWK65SLekJtLEecYbm+0+/v5XxYp7 uRXNu5/TiExV23ehYGcKh1qNADGxDZo0OQ+H8ZSXFTHw3zsjc8zVUBLKMHdqoHK2bJD4 hGww== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=uV9J60wXEm55wLqIR3zB80d1Sl46wMxTOfb2GfAMYO0=; b=EYLNqLOPszssn5/2GThejasLN4vH5bLPSZHeoUpxF8lmxCtchY8WTGSQIEMElVVDn6 XOJ3PFDAiA9Ds78FtxesxEYRVhAFkZx5tpbXTGQfyRJONGvfiOhi2n4FfhLINf5URk9Z KAfhygtmhFAMEeL6KsW9mWN6IK+9VPdEZlDatZFKBfLXdrd9qNNTx1HftTaoVKCfk9WV QxXpXgDoBFy9wlz///VvoRLSM6jUhDa5SrUNC2Ogq3AQI0jsRDGMPtf1CYR00Nsg3Ptw Q7dIwqxwyjx4/9cgQqHvKQf3B6vB/7c6S5a5c4qB7ABCJRqesNBbGtNyjsza6CrLcYNR 7Hmw== X-Gm-Message-State: AOAM532XloYI1Xyf4C+wsZ4dn+Ce6t9Arbgf3ZH7QK5ElMYeTZgzumAa 0F64awHwy3MPoorK7/6qM55ppc/cxL0= X-Google-Smtp-Source: ABdhPJw+jHmMkMLRxzbyD54P1njnaL/VP5j06dYFJwikkhBhgzN05vHhl12mG+5RQOt1FhdwcCzo5w== X-Received: by 2002:a05:600c:410a:: with SMTP id j10mr10586240wmi.5.1621628800928; Fri, 21 May 2021 13:26:40 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:40 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:44 +0200 Message-Id: <20210521202622.26591-12-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-genomation): Move from here... * gnu/packages/bioconductor.scm (r-genomation): ...to here. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 48 --------------------------------- 2 files changed, 48 insertions(+), 48 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eb73909723..2be7920770 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2099,6 +2099,54 @@ CAGE.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-genomation + (package + (name "r-genomation") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "genomation" version)) + (sha256 + (base32 + "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-data-table" ,r-data-table) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-gridbase" ,r-gridbase) + ("r-impute" ,r-impute) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-plotrix" ,r-plotrix) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-readr" ,r-readr) + ("r-reshape2" ,r-reshape2) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-runit" ,r-runit) + ("r-s4vectors" ,r-s4vectors) + ("r-seqpattern" ,r-seqpattern))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") + (synopsis "Summary, annotation and visualization of genomic data") + (description + "This package provides a package for summary and annotation of genomic +intervals. Users can visualize and quantify genomic intervals over +pre-defined functional regions, such as promoters, exons, introns, etc. The +genomic intervals represent regions with a defined chromosome position, which +may be associated with a score, such as aligned reads from HT-seq experiments, +TF binding sites, methylation scores, etc. The package can use any tabular +genomic feature data as long as it has minimal information on the locations of +genomic intervals. In addition, it can use BAM or BigWig files as input.") + (license license:artistic2.0))) + (define-public r-genomeinfodb (package (name "r-genomeinfodb") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 71f07748b6..f8e7b2cab9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,54 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomation - (package - (name "r-genomation") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "genomation" version)) - (sha256 - (base32 - "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-plotrix" ,r-plotrix) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-runit" ,r-runit) - ("r-s4vectors" ,r-s4vectors) - ("r-seqpattern" ,r-seqpattern))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioinformatics.mdc-berlin.de/genomation/") - (synopsis "Summary, annotation and visualization of genomic data") - (description - "This package provides a package for summary and annotation of genomic -intervals. Users can visualize and quantify genomic intervals over -pre-defined functional regions, such as promoters, exons, introns, etc. The -genomic intervals represent regions with a defined chromosome position, which -may be associated with a score, such as aligned reads from HT-seq experiments, -TF binding sites, methylation scores, etc. The package can use any tabular -genomic feature data as long as it has minimal information on the locations of -genomic intervals. In addition, it can use BAM or BigWig files as input.") - (license license:artistic2.0))) - (define-public r-genomationdata (package (name "r-genomationdata")