From patchwork Wed Dec 4 08:57:35 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Efraim Flashner X-Patchwork-Id: 16374 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 640F31783F; Wed, 4 Dec 2019 09:03:53 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 25BB11782F for ; Wed, 4 Dec 2019 09:03:53 +0000 (GMT) Received: from localhost ([::1]:35910 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1icQZb-000524-NU for patchwork@mira.cbaines.net; Wed, 04 Dec 2019 04:03:51 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:46566) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1icQV7-0003RT-JA for guix-patches@gnu.org; Wed, 04 Dec 2019 03:59:17 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1icQUy-0007Vw-Dq for guix-patches@gnu.org; Wed, 04 Dec 2019 03:59:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:35452) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1icQUy-0007Qy-98 for guix-patches@gnu.org; Wed, 04 Dec 2019 03:59:04 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1icQUw-0000Ad-6k for guix-patches@gnu.org; Wed, 04 Dec 2019 03:59:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#38489] [PATCH] gnu: Add r-qtl2. Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 04 Dec 2019 08:59:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 38489 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 38489@debbugs.gnu.org Cc: Efraim Flashner X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.1575449937638 (code B ref -1); Wed, 04 Dec 2019 08:59:02 +0000 Received: (at submit) by debbugs.gnu.org; 4 Dec 2019 08:58:57 +0000 Received: from localhost ([127.0.0.1]:41425 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1icQUr-0000AB-Bs for submit@debbugs.gnu.org; Wed, 04 Dec 2019 03:58:57 -0500 Received: from lists.gnu.org ([209.51.188.17]:58180) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1icQUo-00009p-3G for submit@debbugs.gnu.org; Wed, 04 Dec 2019 03:58:54 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:45640) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1icQUi-0003Ff-Ob for guix-patches@gnu.org; Wed, 04 Dec 2019 03:58:50 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1icQUb-0006Fq-HJ for guix-patches@gnu.org; Wed, 04 Dec 2019 03:58:44 -0500 Received: from flashner.co.il ([178.62.234.194]:51030) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1icQUb-0004dO-AW for guix-patches@gnu.org; Wed, 04 Dec 2019 03:58:41 -0500 Received: from localhost (unknown [141.226.13.108]) by flashner.co.il (Postfix) with ESMTPSA id 18AD44020F; Wed, 4 Dec 2019 08:58:07 +0000 (UTC) From: Efraim Flashner Date: Wed, 4 Dec 2019 10:57:35 +0200 Message-Id: <20191204085735.23318-1-efraim@flashner.co.il> X-Mailer: git-send-email 2.24.0 MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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-qtl2): New variable. --- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b0d070b4e7..522cde959e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8239,6 +8239,35 @@ identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.") (license license:gpl3))) +(define-public r-qtl2 + (package + (name "r-qtl2") + (version "0.20") + (source (origin + (method git-fetch) + ;; Not yet available in cran. + (uri (git-reference + (url "https://github.com/rqtl/qtl2.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0l1asr28q25jzbwrbg5490962sg3y4sjrd0qf09p78ws1aq8vfs0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-jsonlite" ,r-jsonlite) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rsqlite" ,r-rsqlite) + ("r-yaml" ,r-yaml))) + (home-page "https://kbroman.org/qtl2/") + (synopsis + "QTL analysis software for high-dimensional data and complex cross designs") + (description + "R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software +R/qtl, to better handle high-dimensional data and complex cross designs.") + (license license:gpl3))) + (define-public r-zlibbioc (package (name "r-zlibbioc")