From patchwork Tue Jan 21 12:23:32 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Alexis Simon X-Patchwork-Id: 37299 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 1C5E627BBE9; Tue, 21 Jan 2025 12:26:24 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED 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 15A0D27BBE2 for ; Tue, 21 Jan 2025 12:26:21 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1taDKX-0000NP-Ih; Tue, 21 Jan 2025 07:26:05 -0500 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 1taDKV-0000N8-4O for guix-patches@gnu.org; Tue, 21 Jan 2025 07:26:03 -0500 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 1taDKU-0001IT-MM for guix-patches@gnu.org; Tue, 21 Jan 2025 07:26:02 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:Date:From:To:Subject; bh=vIcv92f45omMnYAnF/SRupTlnmkFDHALkBcAc0WodoM=; b=a5Cdw11lKRfbzopqBcwqfkuFe2of7JKzNbaZc9UuOdvMb/Z+poL895Oa93n+lfJHu0fxR3OjFog24vtand9o713qG8o11TVUKjTcFOkB03JljH/tYnl6zGBDeDXjHhc+ygnDSuYgmBs7E13rQ86K8GjD1GNBD83Yu9rHMGwty/zJBWGRNIqdNup3N00xqXzVCrR3A7SynlGvsPBMqkBIWfVZvsusali7kf41HGEus4XKctpEUGVAEjkm8lvUsiq0hXTuz5VcbSkKwNnw4fUKfRKnmcgAFwtvJS5XHLgDHYbBASQ4FA0inE2sfCchcggIx+QebilE1dcbimULV9wZ2A==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1taDKU-0008Eo-81 for guix-patches@gnu.org; Tue, 21 Jan 2025 07:26:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#75727] [PATCH] gnu: Add r-sigfit. Resent-From: Alexis Simon Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 21 Jan 2025 12:26:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 75727 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 75727@debbugs.gnu.org Cc: Alexis Simon X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.173746230631333 (code B ref -1); Tue, 21 Jan 2025 12:26:02 +0000 Received: (at submit) by debbugs.gnu.org; 21 Jan 2025 12:25:06 +0000 Received: from localhost ([127.0.0.1]:53512 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1taDJZ-00088w-Ug for submit@debbugs.gnu.org; Tue, 21 Jan 2025 07:25:06 -0500 Received: from lists.gnu.org ([2001:470:142::17]:58436) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1taDJX-00086P-1f for submit@debbugs.gnu.org; Tue, 21 Jan 2025 07:25:04 -0500 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 1taDJO-0000Dk-Ey for guix-patches@gnu.org; Tue, 21 Jan 2025 07:24:54 -0500 Received: from mailtransmit05.runbox.com ([2a0c:5a00:149::26]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1taDJJ-0000vq-DP for guix-patches@gnu.org; Tue, 21 Jan 2025 07:24:54 -0500 Received: from mailtransmit02.runbox ([10.9.9.162] helo=aibo.runbox.com) by mailtransmit05.runbox.com with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256 (Exim 4.93) (envelope-from ) id 1taDJA-000mil-SS for guix-patches@gnu.org; Tue, 21 Jan 2025 13:24:40 +0100 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=runbox.com; s=selector2; h=Content-Transfer-Encoding:MIME-Version:Message-ID:Date: Subject:Cc:To:From; bh=vIcv92f45omMnYAnF/SRupTlnmkFDHALkBcAc0WodoM=; b=Ayjixy uTzU0F0x2TZnviX2+tHfO8GQ1Z1ua1Az2WbB4JcjskN1iL6oyDlHInwtzB9NlwlMrJ0Ru17JAjMAc Ja54qjt3zOUNilr8gtSqM5NRbq0N2wnqw9zw8KkG0bO/RKL19KARvOOiKFAc60hBvegQZyXRWcqkb stYlB3+C9BS4fQ2tspR1MpVOHBbr+ZJHyGFdapgX2ieZ+/VRMOQ8FywjFBxcDL16gPQcM1G+Xvixf Vt5lOPD3F0+cj66wf96uwj2giz8LwurZiaoc6h/avVs5oOcXM0Qeacx+DG9lbmvoZP57gdG9w+nSW x09RV/zBqrP9rPfZ4ny+HM4lcBMQ==; Received: from [10.9.9.74] (helo=submission03.runbox) by mailtransmit02.runbox with esmtp (Exim 4.86_2) (envelope-from ) id 1taDJA-0001Vd-H1 for guix-patches@gnu.org; Tue, 21 Jan 2025 13:24:40 +0100 Received: by submission03.runbox with esmtpsa [Authenticated ID (1174703)] (TLS1.2:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.93) id 1taDIu-00BLdV-G3; Tue, 21 Jan 2025 13:24:24 +0100 Date: Tue, 21 Jan 2025 13:23:32 +0100 Message-ID: X-Mailer: git-send-email 2.45.2 MIME-Version: 1.0 Received-SPF: pass client-ip=2a0c:5a00:149::26; envelope-from=alexis.simon@runbox.com; helo=mailtransmit05.runbox.com X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 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, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_LOW=-0.7, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action 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: , Reply-to: Alexis Simon X-ACL-Warn: , Alexis Simon via Guix-patches X-Patchwork-Original-From: Alexis Simon via Guix-patches via From: Alexis Simon 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 * gnu/packages/bioinformatics.scm (r-sigfit): New variable. Change-Id: I9d63975d3512cf8583e7ec22f450bb4963c9ff2f --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) base-commit: cf34ba66cf614358dfac925212d6a9074e318d80 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c98f6022bf..899606b195 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1526,6 +1526,42 @@ (define-public r-saige tests in large cohorts and biobanks (SAIGE-GENE+).") (license license:gpl2+)))) +(define-public r-sigfit + (package + (name "r-sigfit") + (version "2.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kgori/sigfit") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "16r6m8p90rnb4hxl86fz3kbals3626232i8fj0zhhd23p89z3w4v")))) + (properties `((upstream-name . "sigfit"))) + (build-system r-build-system) + (native-inputs (list r-codetools)) + (propagated-inputs (list r-rcpp + r-rstan + r-rstantools + r-coda + r-clue + r-knitr + r-rmarkdown + r-bh + r-rcppeigen + r-stanheaders)) + (home-page "https://github.com/kgori/sigfit") + (synopsis "Flexible Bayesian inference of mutational signatures") + (description + "R package to estimate signatures of mutational processes and their +activities on mutation count data. Starting from a set of single-nucleotide +variants (SNVs), it allows both estimation of the exposure of samples to +predefined mutational signatures (including whether the signatures are +present at all), and identification of signatures de novo from the mutation counts.") + (license license:gpl3))) + (define-public r-singlet (let ((commit "765a6c45081807a1522f0e8983e2417822a36f36") (revision "1"))