From patchwork Fri May 21 20:25:38 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29474 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 B8B9527BC81; Fri, 21 May 2021 21:30:42 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4, RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A6FB127BC78 for ; Fri, 21 May 2021 21:30:41 +0100 (BST) Received: from localhost ([::1]:41112 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBn6-00006K-NQ for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:30:40 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52416) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkY-0004HC-Rm for guix-patches@gnu.org; Fri, 21 May 2021 16:28:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54482) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkY-0002vg-KF for guix-patches@gnu.org; Fri, 21 May 2021 16:28:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkY-0000LM-Gk for guix-patches@gnu.org; Fri, 21 May 2021 16:28:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 06/50] gnu: r-msnid: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:02 +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=B48575.1621628829903 (code B ref 48575); Fri, 21 May 2021 20:28:02 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:09 +0000 Received: from localhost ([127.0.0.1]:37683 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjU-0000CX-FH for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:09 -0400 Received: from mail-wm1-f50.google.com ([209.85.128.50]:35342) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjH-00008W-Pa for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:44 -0400 Received: by mail-wm1-f50.google.com with SMTP id z19-20020a7bc7d30000b029017521c1fb75so8082861wmk.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:43 -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=tc7IxdTSryxu41PLiIjT5EDICeRvUfP0FHfUM2vWOXo=; b=gjxnfeuWkD/DbxfgGS5wvEBrwjwj/3f4FlnirQ/kia7NOQYpP3Dn9lxKPbVlMyRQ5n LLIyNTnrFzGltRWJZpbfQXX6BE/mSTOcwwKDBhmvldjZ3MeX4coZmJpUJvGOksygxVI9 B3sU2ScE4w49KNy9e/YOwm1+Ix7zqgHM9lFl4/tlmv+ngwFakVyUoj6z8NcXGTUlahnW Q/6UxJK7wiAbBph72Bx0QKDYgHulohoMACFnaRX3oMBrg+aqWs5UVQ0F6n2xtOgZVFKS IL+UW0bvICCavUnn7XStmE+y0hILuiQi+T/ypSSE1Cc609qmk31LgQbkDoaQPuZvXZSf a3VQ== 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=tc7IxdTSryxu41PLiIjT5EDICeRvUfP0FHfUM2vWOXo=; b=N9OwlXAZM0Q/Q5Dpr71B2J4PDF1cTPO2xCzBV9sejZNHJWV58pggEsUT4hzikt05qS ylB2aTcFYtGb8sK5V/+iY2n7UT2LI7VQC2YI5HSsLuF5Wyw8IO4xpdepRvBSTkGOcKGl 8Q5kMF99bNwcvJptt5WmNISdPs8DcVIhR1JqaNh3LpPv4cwgm/wRVSTsXBOHY4w1Je0E 7FKUvFGhMyM5DdVJMWjGoHTTaXc1HICIH/5NAuss3zTjF4htDpaecV2Qsn01RGZfwXaZ Lm2f70tElcAvSzlwfzHNPlucsyd05ilfImwV9bPEZPX3ERMEq76FkB3T/h1a7Bhrsh/K MUVQ== X-Gm-Message-State: AOAM531GttB002QR+7QM5ERQK8t63ICSEZ3iWf3EuSilm4VhajwLEe9T aO9vhG5xNhZ8e2QHuJLTsTNycMngeVg= X-Google-Smtp-Source: ABdhPJwksGfDHxjEb59+pWIH5RZcobe3OElguI+Y8zYqV8bI6fm/a7gIXGLl91FAxLFwG8j2ypul+A== X-Received: by 2002:a05:600c:4f8f:: with SMTP id n15mr2925612wmq.107.1621628798155; Fri, 21 May 2021 13:26:38 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.37 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:37 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:38 +0200 Message-Id: <20210521202622.26591-6-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-msnid): Move from here... * gnu/packages/bioconductor.scm (r-msnid): ...to here. --- gnu/packages/bioconductor.scm | 52 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 52 --------------------------------- 2 files changed, 52 insertions(+), 52 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 923413135b..b5787cb207 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2312,6 +2312,58 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-msnid + (package + (name "r-msnid") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MSnID" version)) + (sha256 + (base32 + "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d")))) + (properties `((upstream-name . "MSnID"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocstyle" ,r-biocstyle) + ("r-biostrings" ,r-biostrings) + ("r-data-table" ,r-data-table) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-iterators" ,r-iterators) + ("r-msnbase" ,r-msnbase) + ("r-msmstests" ,r-msmstests) + ("r-mzid" ,r-mzid) + ("r-mzr" ,r-mzr) + ("r-protgenerics" ,r-protgenerics) + ("r-purrr" ,r-purrr) + ("r-r-cache" ,r-r-cache) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-runit" ,r-runit) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-xtable" ,r-xtable))) + (home-page "https://bioconductor.org/packages/MSnID") + (synopsis "Utilities for LC-MSn proteomics identifications") + (description + "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data +from mzIdentML (leveraging the mzID package) or text files. After collating +the search results from multiple datasets it assesses their identification +quality and optimize filtering criteria to achieve the maximum number of +identifications while not exceeding a specified false discovery rate. It also +contains a number of utilities to explore the MS/MS results and assess missed +and irregular enzymatic cleavages, mass measurement accuracy, etc.") + (license license:artistic2.0))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9c9288c6b0..5c2abe6e94 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9275,58 +9275,6 @@ structure (pcaRes) to provide a common interface to the PCA results.") of mass spectrometry based proteomics data.") (license license:artistic2.0))) -(define-public r-msnid - (package - (name "r-msnid") - (version "1.24.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MSnID" version)) - (sha256 - (base32 - "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d")))) - (properties `((upstream-name . "MSnID"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-msnbase" ,r-msnbase) - ("r-msmstests" ,r-msmstests) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-protgenerics" ,r-protgenerics) - ("r-purrr" ,r-purrr) - ("r-r-cache" ,r-r-cache) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-runit" ,r-runit) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xtable" ,r-xtable))) - (home-page "https://bioconductor.org/packages/MSnID") - (synopsis "Utilities for LC-MSn proteomics identifications") - (description - "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data -from mzIdentML (leveraging the mzID package) or text files. After collating -the search results from multiple datasets it assesses their identification -quality and optimize filtering criteria to achieve the maximum number of -identifications while not exceeding a specified false discovery rate. It also -contains a number of utilities to explore the MS/MS results and assess missed -and irregular enzymatic cleavages, mass measurement accuracy, etc.") - (license license:artistic2.0))) - (define-public r-aroma-light (package (name "r-aroma-light")