From patchwork Sat May 18 07:50:46 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: "ashish.is--- via Guix-patches\" via" X-Patchwork-Id: 27635 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 73DA927BBE9; Sat, 18 May 2024 14:15:52 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.6 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED,URIBL_SBL_A autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id B94D127BBE2 for ; Sat, 18 May 2024 14:15:49 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1s8Ju3-0008CX-MH; Sat, 18 May 2024 09:15:11 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1s8GiU-0003du-9N for guix-patches@gnu.org; Sat, 18 May 2024 05:51:03 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1s8GiS-0000Z5-DB for guix-patches@gnu.org; Sat, 18 May 2024 05:51:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1s8GiV-0000g9-Mg for guix-patches@gnu.org; Sat, 18 May 2024 05:51:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#71031] [PATCH] Added r-mcview Resent-From: guix@mawumag.com Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 18 May 2024 09:51:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 71031 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 71031@debbugs.gnu.org Cc: rekado@elephly.net X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.17160258102549 (code B ref -1); Sat, 18 May 2024 09:51:03 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2024 09:50:10 +0000 Received: from localhost ([127.0.0.1]:60682 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s8Ghd-0000ew-Aa for submit@debbugs.gnu.org; Sat, 18 May 2024 05:50:10 -0400 Received: from lists.gnu.org ([209.51.188.17]:60052) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s8EqO-00076a-8u for submit@debbugs.gnu.org; Sat, 18 May 2024 03:51:05 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1s8EqJ-0002K7-RX for guix-patches@gnu.org; Sat, 18 May 2024 03:50:59 -0400 Received: from mail-200162.simplelogin.co ([176.119.200.162]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1s8EqF-000431-Cr for guix-patches@gnu.org; Sat, 18 May 2024 03:50:57 -0400 ARC-Seal: i=1; a=rsa-sha256; d=simplelogin.co; s=arc-20230626; t=1716018650; cv=none; b=Jpq5j6Rz+4weQeWMel3QIwUtrQOMx+0K3roktYIi5eVGvfzZJDxoeGsEdajfN6HbpVztIWB/10X9koHb+Q6fkT0j4IjY4NzL9xSsM7FIkF68xMkap3SaN/HeKxsjLI4B9GAYVBoaCrDqAnFrBBX/HohFeEOgYKtpVwM+w5QCOIOVBWkJa0Zm4qyH+IjlTQHUbqcGxp8TO//THjVsH5tQGR6LY3PTyk1Hx96l1ODlTx/CYFhvqxIV3rXMVohUn9ta9U/OgwqNhOsKYnYBN2FnmVBVPvFY7DMzdyP0cs8/rJJhvhVkDqlL5WfVQ+Rq+St9sPj1QvyKS8NmLBq2rc94pg== ARC-Message-Signature: i=1; a=rsa-sha256; d=simplelogin.co; s=arc-20230626; t=1716018650; c=relaxed/simple; bh=oTBWDJulpADsT4o21nCW3Ns4K5JLcehGUUx9QFkDnRw=; h=Date:Subject:From:To:Cc; b=tgxQwC9SRnbaecwBIU4cdPKgoYDtvO0nkINyIM0WlgaAn+Ws7zM++fPgvBGXO16T6n/m/AiKDQQ4lF5auLAtgBzsWcUVcP6Cnuc0lqZEeVpE4vIyLbONpenjmcRvkRgSHf5rcyWvbHDIcMzfxYIfGi1aimNa6Sp/oIV3WzuLAU+jDB0zGacLsY1Oa+UsuRCxnqZRfTW+f129l53RA4Ujb37exDbnjWhnn+FH48zZNc0kra5djvrGIC7kw1NvDGQBb6VwQVWI1rBpQ4MxUZ9uzjqZ1FdP1rujmUMXJL/IBxtrDKPLMKA4xmD89Ys+GArMEn20cBeGIPBxCu7lfIxo6A== ARC-Authentication-Results: i=1; mail.protonmail.ch DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mawumag.com; s=dkim; t=1716018650; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=l8Z0nJKsqnKJgKbcL3G8LldWO7XfmkL0TBlK4U1MG/s=; b=AU8E6G6nx3vhSbZnUQt0Gw68rGY209nRf2kehUle/Bu+POOg1BavVuuy7Vi3trn/eHpUOH bJoAJiFUS8WtLeXV/MiCtGrwuRlt7mJZYbi8EgBpUdMImeIboBzlu16BoK83UFdm2aN8LQ 0jeug3OyOKc3v8poLThOR618xmqmhPM= Date: Sat, 18 May 2024 07:50:46 +0000 MIME-Version: 1.0 Message-ID: <171601865003.8.3299177765362446936.333610631@mawumag.com> X-SimpleLogin-Type: Reply X-SimpleLogin-EmailLog-ID: 333610632 X-SimpleLogin-Want-Signing: yes Received-SPF: pass client-ip=176.119.200.162; envelope-from=sl.lmysyibtgmztmmjqgyztelbagezdkmbtheyf2.r23xvxhoioo6i@mawumag.com; helo=mail-200162.simplelogin.co X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Mailman-Approved-At: Sat, 18 May 2024 05:50:05 -0400 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Mailman-Approved-At: Sat, 18 May 2024 09:15:09 -0400 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: guix@mawumag.com X-ACL-Warn: , guix--- via Guix-patches X-Patchwork-Original-From: guix--- via Guix-patches via From: "ashish.is--- via Guix-patches\" via" Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches From b6eec887067b4c4697fad3cae4f11fabc6330a86 Mon Sep 17 00:00:00 2001 From: Marco Baggio Date: Sat, 18 May 2024 09:23:07 +0200 Subject: [PATCH] Added r-mcview Change-Id: I377b7fd2256215ddcad73f4263bab251bd4319cd --- I added the package MCView, used to generate shiny apps for metacell models, as well as dependencies not yet present in the official Guix repository. --- gnu/packages/bioinformatics.scm | 314 ++++++++++++++++++++++++++++++++ 1 file changed, 314 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6aa35710e5..a696a5df29 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12228,6 +12228,320 @@ (define-public r-shinycell single-cell data.") (license license:gpl3)))) +(define-public r-mcview + (let ((commit "85a61fe6efa241ac72f79fb965c3227538ead518") + (revision "1")) + (package + (name "r-mcview") + (version (git-version "0.2.28" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tanaylab/MCView") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "187q6qy8ss0g6h3c0ckw9ypq8615bk5yypfl5l4rq6dzaflm4iba")))) + (properties `((upstream-name . "MCView"))) + (build-system r-build-system) + (propagated-inputs (list r-anndata + r-cachem + r-chameleon + r-circlize + r-cli + r-colourpicker + r-cowplot + r-dplyr + r-dt + r-fastcluster + r-forcats + r-fs + r-furrr + r-future + r-gert + r-ggplot2 + r-ggtext + r-glue + r-golem + r-htmltools + r-markdown + r-matrix + r-matrixstats + r-pkgload + r-plotly + r-promises + r-purrr + r-qs + r-rintrojs + r-rlang + r-rmarkdown + r-scales + r-shiny + r-shinybusy + r-shinycssloaders + r-shinydashboard + r-shinydashboardplus + r-shinyjqui + r-shinyjs + r-shinywidgets + r-slanter + r-tglkmeans + r-tgstat + r-tgutil + r-tibble + r-tidyr + r-umap + r-viridis + r-waiter + r-yaml + r-zip)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tanaylab/MCView") + (synopsis "Shiny App for Metacell Analysis") + (description + "MCView creates a shiny-app facilitating interactive exploration and annotation +of metacell models. Metacell itself is described +[here](https://github.com/tanaylab/metacells/blob/master/vignettes/Metacells_Vignette.ipynb). + You can also explore examples of MCV output for +[PBMC](https://tanaylab.weizmann.ac.il/MCV/PBMC) and [Mouse +organogenesis](https://tanaylab.weizmann.ac.il/MCV/MOCA) on the Tanay group +server.") + (license license:expat)))) + +(define-public r-chameleon + (package + (name "r-chameleon") + (version "0.2-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "chameleon" version)) + (sha256 + (base32 "0a3azp0zaakpqqx0pp94hkj3vgb2apnf8gb5ga0as4i8lrn9dz8i")))) + (properties `((upstream-name . "chameleon"))) + (build-system r-build-system) + (propagated-inputs (list r-clue r-ggplot2 r-umap)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=chameleon") + (synopsis "Automatic Colors for Multi-Dimensional Data") + (description + "Assign distinct colors to arbitrary multi-dimensional data, considering its +structure.") + (license license:expat))) + +(define-public r-shinybusy + (package + (name "r-shinybusy") + (version "0.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinybusy" version)) + (sha256 + (base32 "1bjfi5xdidj8n84mylghvrncvcyg625kj8pnizl59m649k3n10v2")))) + (properties `((upstream-name . "shinybusy"))) + (build-system r-build-system) + (propagated-inputs (list r-htmltools r-htmlwidgets r-jsonlite r-shiny)) + (native-inputs (list esbuild r-knitr)) + (home-page "https://github.com/dreamRs/shinybusy") + (synopsis "Busy Indicators and Notifications for 'Shiny' Applications") + (description + "Add indicators (spinner, progress bar, gif) in your shiny applications to show +the user that the server is busy. And other tools to let your users know +something is happening (send notifications, reports, ...).") + (license license:gpl3))) + +(define-public r-shinydashboardplus + (package + (name "r-shinydashboardplus") + (version "2.0.3") + (source (origin + (method url-fetch) + (uri (cran-uri "shinydashboardPlus" version)) + (sha256 + (base32 + "10sdb1vddx2ij867pqijr63l4233hw1vnn7mzbs0z23g77x8ra29")) + (modules '((guix build utils))) + (snippet + `(begin + (with-directory-excursion + ,(string-append "inst/shinydashboardPlus-" version + "/js/") + (for-each delete-file + '("app.min.js" + "shinydashboardPlus.min.js" + "shinydashboardPlus.min.js.map"))) + (with-directory-excursion "inst/materialDesign-1.0/js" + (for-each delete-file + '("material.min.js" + "ripples.min.js"))))))) + (properties `((upstream-name . "shinydashboardPlus"))) + (build-system r-build-system) + (arguments + (list + #:tests? #false + #:modules + '((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules + `(,@%r-build-system-modules + (guix build minify-build-system)) + #:phases + #~(modify-phases (@ (guix build r-build-system) %standard-phases) + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion + (string-append "inst/shinydashboardPlus-" #$version "/js/") + (for-each + (match-lambda + ((source . target) + (minify source #:target target))) + `(("app.js" . "app.min.js") + ("shinydashboardPlus.js" . "shinydashboardPlus.min.js") + (,(search-input-file inputs "/dist/js/material.js") + . "materialDesign-1.0/js/material.min.js") + (,(search-input-file inputs "/dist/js/ripples.js") + . "materialDesign-1.0/js/ripples.min.js"))))))))) + (propagated-inputs + (list r-fresh + r-htmltools + r-lifecycle + r-shiny + r-shinydashboard + r-waiter)) + (native-inputs + (list esbuild + r-knitr + (let ((commit "92a2284b47aed56a9d7ae92cf9b40072d27982b3")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DucThanhNguyen/MaterialAdminLTE") + (commit commit))) + (file-name (git-file-name "MaterialAdminLTE" + (git-version "0" "0" commit))) + (sha256 + (base32 + "0cn11hxpf25h7xj2lk473z24swgz979dz255zwk2m2fj00iljkn9")))))) + (home-page "https://github.com/RinteRface/shinydashboardPlus") + (synopsis "Add more AdminLTE2 components to shinydashboard") + (description + "This package extends shinydashboard with AdminLTE2 components. +AdminLTE2 is a Bootstrap 3 dashboard template. Customize boxes, add timelines +and a lot more.") + (license license:gpl2+))) + +(define-public r-shinywidgets + (package + (name "r-shinywidgets") + (version "0.8.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyWidgets" version)) + (sha256 + (base32 "02z8fwvnmi6lacqi6ryxssm1w3mh4vfphjrp3v1d6dij3s3l6z0q")))) + (properties `((upstream-name . "shinyWidgets"))) + (build-system r-build-system) + (propagated-inputs + (list r-anytime + r-bslib + r-htmltools + r-jsonlite + r-rlang + r-sass + r-shiny)) + (home-page "https://github.com/dreamRs/shinyWidgets") + (synopsis "Custom inputs widgets for Shiny") + (description + "This package provides a collection of custom input controls and user +interface components for Shiny applications.") + (license license:gpl3))) + +(define-public r-slanter + (package + (name "r-slanter") + (version "0.2-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "slanter" version)) + (sha256 + (base32 "024dkman0r5qzc215gw0ds932vdaz8krrhv64fjw9pni37ixc3mf")))) + (properties `((upstream-name . "slanter"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-pheatmap r-pracma)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=slanter") + (synopsis "Slanted Matrices and Ordered Clustering") + (description + "Slanted matrices and ordered clustering for better visualization of similarity +data.") + (license license:expat))) + +(define-public r-tglkmeans + (package + (name "r-tglkmeans") + (version "0.5.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "tglkmeans" version)) + (sha256 + (base32 "1plg03k9r4sp8ck5qcj8shblr8378bynyyc7yqwcqv856vkl9icd")))) + (properties `((upstream-name . "tglkmeans"))) + (build-system r-build-system) + (propagated-inputs (list r-cli + r-dofuture + r-dplyr + r-future + r-ggplot2 + r-magrittr + r-matrix + r-metacell + r-plyr + r-purrr + r-rcpp + r-rcppparallel + r-tgstat + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://tanaylab.github.io/tglkmeans/") + (synopsis "Efficient Implementation of K-Means++ Algorithm") + (description + "Efficient implementation of K-Means++ algorithm. For more information see (1) +\"kmeans++ the advantages of the k-means++ algorithm\" by David Arthur and Sergei +Vassilvitskii (2007), Proceedings of the eighteenth annual ACM-SIAM symposium on +Discrete algorithms, Society for Industrial and Applied Mathematics, +Philadelphia, PA, USA, pp. 1027-1035, and (2) \"The Effectiveness of Lloyd-Type +Methods for the k-Means Problem\" by Rafail Ostrovsky, Yuval Rabani, Leonard J. +Schulman and Chaitanya Swamy .") + (license license:expat))) + +(define-public r-waiter + (package + (name "r-waiter") + (version "0.2.5") + (source (origin + (method url-fetch) + (uri (cran-uri "waiter" version)) + (sha256 + (base32 + "0ya92qr25ssfkzn888b7rr8rn0304f3gz4h4pnc2a95rknbmxhls")))) + (properties `((upstream-name . "waiter"))) + (build-system r-build-system) + (propagated-inputs (list r-htmltools r-r6 r-shiny)) + (native-inputs (list r-knitr)) + (home-page "https://waiter.john-coene.com/") + (synopsis "Loading screen for Shiny") + (description + "This package provides full screen and partial loading screens +for Shiny with spinners, progress bars, and notifications.") + (license license:expat))) + (define-public r-archr (let ((commit "c61b0645d1482f80dcc24e25fbd915128c1b2500") (revision "1"))