From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp11.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms9.migadu.com with LMTPS id 0NMxB4EWXmQsCQAASxT56A (envelope-from ) for ; Fri, 12 May 2023 12:35:45 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp11.migadu.com with LMTPS id WP8tB4EWXmSe7gAA9RJhRA (envelope-from ) for ; Fri, 12 May 2023 12:35:45 +0200 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id D1ADD11AAF for ; Fri, 12 May 2023 12:35:44 +0200 (CEST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pxQ7A-0005kN-W3; Fri, 12 May 2023 06:35:09 -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 1pxQ75-0005jx-Ni for guix-patches@gnu.org; Fri, 12 May 2023 06:35:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pxQ75-0007zK-D5 for guix-patches@gnu.org; Fri, 12 May 2023 06:35:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pxQ74-0005kO-J2 for guix-patches@gnu.org; Fri, 12 May 2023 06:35:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63448] [PATCH v2 2/2] gnu: Add python-mgatk. References: <271d6a24b07a43ce8258824917b6630a@mdc-berlin.de> In-Reply-To: <271d6a24b07a43ce8258824917b6630a@mdc-berlin.de> Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 12 May 2023 10:35:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 63448 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <63448@debbugs.gnu.org> Received: via spool by 63448-submit@debbugs.gnu.org id=B63448.168388766222032 (code B ref 63448); Fri, 12 May 2023 10:35:02 +0000 Received: (at 63448) by debbugs.gnu.org; 12 May 2023 10:34:22 +0000 Received: from localhost ([127.0.0.1]:54117 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pxQ6P-0005jH-N8 for submit@debbugs.gnu.org; Fri, 12 May 2023 06:34:22 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:56865) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pxQ6M-0005j2-73 for 63448@debbugs.gnu.org; Fri, 12 May 2023 06:34:20 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1683887650; x=1685702051; bh=MrEGrVAKeNkTL3V P0SAEKd2QwbCsSCqzF31u4GoKnrE=; b=jjkiUYGfkgAMLB3BR22UsCN48AkH1ZP o2WKbJUfn/3tED+hZ5Aj0xxzmZAEr+VyQ+Xll/Jz1wBQTcTeuZEf1BhRGxWdFHMn nwxTdUy6ebKDP5e+kfiM9yKDGdS5xYLpREDjOsmJRj4xBX4CBPuc11Y6xumkxD1U rhq4IWtMhdXA= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id C8C07A0184 for <63448@debbugs.gnu.org>; Fri, 12 May 2023 12:34:10 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.23; Fri, 12 May 2023 12:34:10 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Fri, 12 May 2023 12:33:59 +0200 Message-ID: <20230512103359.4111-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27620.006 X-TM-AS-Result: No-10--9.418000-5.000000 X-TMASE-MatchedRID: huMMtcahIlB6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896shuUivRMGUl1mtEzrC9eANpR5O 2+B+mEplaaTQaF8Q9iMyztI3jcIWiJVWqk0NljVw8o3fwIs8rQXM0J0a6ZmxJ33Nl3elSfsrcar 0PoQvHhpA8bj4Y6Py0DNGOMXPJrk3GfM7IyIraCdfeP+V/VXwslKvhkP88iXQ6FHRWx2FGsNM5c V34PBF5XYNtPHirFUB22LX9ExaXqtaVXJCx4JNCq5uw61JZjZCAMuqetGVetnyef22ep6XYymsk /wUE4hqKvpFqp0OEvhLLsrt/WKrHSUL5gdykj1QD70l9LpgWO4XuAoQABClJ X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--9.418000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27620.006 X-TM-SNTS-SMTP: 42E28ED8BDF493A93476905194068B5F524E76F4FC280A078A98241632A85EBD2002:F 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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN ARC-Seal: i=1; s=key1; d=yhetil.org; t=1683887744; a=rsa-sha256; cv=none; b=Jf6e1bY8WapetHiFpQHvpa59HL5q8iFkqoEQ94XcoEzTIJJRIHauJf/oW5P3fRQ3hw8E2k talFGWRNil0DOMNA22EZwuJbhVHfZHTLA5dKliI8iV8CFMDCrOelgyRf/1wGsfeTyPEdse MS9x9yoYz95KTgNi0vLQfsunTwvYrXx8OAyoKb8b9taS485dRLVd/G6iprUE7WUHgFSvL5 zfm0MlnvaLyVmWlRC2o+6QlNikAnmkkC+IfGK9OQz1KEtFjlyHK6LW2lQ767JLRtzXDo1L fsHWJPtdsHu6Pj74QRUp8PYcVg6btnS8AXTxnSxn/7D3xnNoUCyB24zOUxSQmA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=jjkiUYGf; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1683887744; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=6dJqKzRhIt0pqr0xcYVX6CBAOFM/8CMO2mKinVcUjbU=; b=FqRmi4QyqukyGZnVGoo/KtY6oZSAalzcggweRV42NG6tTNda3EMts0jbKQTKjhbWp8iPtP 8mGMv+ZRnd2+XQ1yC/i9qiLCr/chZEQCSrUzF0InFgrYjCJPPfzRTWbg1yuphudArSmigr tKAckbfGSJLS98Igg7SNvUo6IRDhTk2dxoX5vWHhps5xobpd3eK4agrMB5kC+Lq2WCoOUE PXoSn/2BuR7DyOclJCqhpTAo5A42ysMpTuaRBKNBsYhKd1ojPB2/QsIHmBqOgoSpJpDiTu YiuQLAyX3efe8P+0mBh4Mwigl4QrjV0M+Jw0Li+kXANCJI+imGyD2HI/6bw5Sw== X-Migadu-Spam-Score: -0.21 X-Spam-Score: -0.21 X-Migadu-Queue-Id: D1ADD11AAF X-Migadu-Scanner: scn0.migadu.com Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=jjkiUYGf; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-TUID: 30BDIG+fSZnf * gnu/packages/bioinformatics.scm (python-mgatk): New variable. --- gnu/packages/bioinformatics.scm | 54 +++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index afca5ab93b..86e54ad5f5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12628,6 +12628,60 @@ (define-public python-biothings-client API services.") (license license:bsd-3))) +(define-public python-mgatk + (let ((commit "2633903acb1fb406bb58c787f320c3641f446ee7") + (revision "0")) + (package + (name "python-mgatk") + (version "0.6.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/caleblareau/mgatk") + (commit commit))) + (file-name (git-file-name name version)) + ;(method url-fetch) + ;(uri (pypi-uri "mgatk" version)) + (sha256 + (base32 "19iklfv1brwsfg1l5lrs3z8m343nskkn1998c1fs7fdn0lgrki2p")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; The md5 module has beed deprecated since Python 2.5 + (add-after 'unpack 'make-python3-compatible + (lambda* _ + (substitute* "tests/test_cli.py" + (("import md5") "")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "-k" "not file_checksums_equal"))))))) + (propagated-inputs + (list python-biopython + python-click + python-numpy + python-optparse-pretty + python-pandas + python-pysam + python-regex + python-ruamel.yaml + snakemake)) + (native-inputs + (list python-minimal + python-pytest)) + (home-page "https://github.com/caleblareau/mgatk") + (synopsis "Mitochondrial genome analysis toolkit.") + (description "This package is a python-based command line interface for +processing .bam files with mitochondrial reads and generating high-quality +heteroplasmy estimation from sequencing data. The mgatk package places a +special emphasis on mitochondrial genotypes generated from single-cell genomics +data, primarily @acronym{mtscATAC-seq, mitochondrial single-cell ATAC-sequence}, +but is generally applicable across other assays.") + (license license:expat)))) + (define-public python-multivelo (package (name "python-multivelo") base-commit: d07342b16612cfdffad6a7b3504b74e0d95d551f -- 2.39.2