From patchwork Thu May 11 18:34:11 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 49940 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 51AD727BBF1; Thu, 11 May 2023 19:35:15 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=ham 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 94A0127BBEE for ; Thu, 11 May 2023 19:35:13 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pxB84-0003ik-Uu; Thu, 11 May 2023 14:35:05 -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 1pxB83-0003ht-Lp for guix-patches@gnu.org; Thu, 11 May 2023 14:35:03 -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 1pxB83-0004X6-CL for guix-patches@gnu.org; Thu, 11 May 2023 14:35:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pxB83-0001VC-08; Thu, 11 May 2023 14:35:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63448] [PATCH 1/2] gnu: Add python-optparse-pretty. References: <271d6a24b07a43ce8258824917b6630a@mdc-berlin.de> In-Reply-To: <271d6a24b07a43ce8258824917b6630a@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Thu, 11 May 2023 18:35:02 +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> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 63448-submit@debbugs.gnu.org id=B63448.16838300865740 (code B ref 63448); Thu, 11 May 2023 18:35:02 +0000 Received: (at 63448) by debbugs.gnu.org; 11 May 2023 18:34:46 +0000 Received: from localhost ([127.0.0.1]:53351 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pxB7l-0001UO-L9 for submit@debbugs.gnu.org; Thu, 11 May 2023 14:34:46 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:58795) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pxB7k-0001Tv-0f for 63448@debbugs.gnu.org; Thu, 11 May 2023 14:34:44 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1683830077; x=1685644478; bh=6V6KaaWXDI0QdAa Iskc6bqIwr2pxci1fYwmvjbXt3Xg=; b=kU0Vladq31VbNC8Z8ccRjTszLYJBUda 2va6Ar3OYzEQ9JkZX6dzBI3+Ump0BZQWp3e0kyA0LJunf4jdACWtMo2aYNAA9nvB Yvyzly4RZGEFRklWK3O5fEzkDssOdi9DQ38XaUFPxyEFfBz24Sga6Q9oVO983g1P 9SjVRJyQaCoI= 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 b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 26DA1160169 for <63448@debbugs.gnu.org>; Thu, 11 May 2023 20:34:37 +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; Thu, 11 May 2023 20:34:36 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 11 May 2023 20:34:11 +0200 Message-ID: <20230511183412.27180-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27620.001 X-TM-AS-Result: No-10--4.820200-5.000000 X-TMASE-MatchedRID: n8dyCgqCzuv/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPONWv RsOl9XyI9ibr3B94ZyzVMFEV5m+G9Sq+GZ9ZHxIhuW77/y896sgxVUWGXs3C8y196sn93sBv+5B GtESW2wa+Cd5IfDKvne8j2/Qpcz4836eSajIECZnjKGx9YdNc4ln4Ir4HFD2Tx8BJ7uScK23Jw6 G9NdOWi5KQhRnJRBQntWKNR2epAFaCWMXx8ovaCefOVcxjDhcwPcCXjNqUmkXCttcwYNipXw2y0 JeZ/zscxn2DIL+YfkVvSuQRYC9dqjQYPnC6gtjvc484ft8EDd2VsdVO/VsmSZnD7U3McwMm9YXZ uysbSjQ48OaUNUSrmjWMuiwuZwzfKEIODKywTy6jfJglXzHQ6sxRVzSzXt2xf+rhMPa/srU= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.820200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27620.001 X-TM-SNTS-SMTP: 3F18F0B4294D8AE64E66CD570DCF11CC6A324781E5441C9021CBE5EB3B1DA61A2002: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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-xyz.scm (python-optparse-pretty): New variable --- gnu/packages/python-xyz.scm | 23 ++++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) base-commit: e2eb43f945fd467e9b55a4b3c91cd186cf32e268 diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4f48d80eb6..9fabfce79f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -66,7 +66,7 @@ ;;; Copyright © 2019, 2020, 2021 Giacomo Leidi ;;; Copyright © 2019 Wiktor Żelazny ;;; Copyright © 2019, 2020, 2021, 2022 Tanguy Le Carrour -;;; Copyright © 2019, 2021, 2022 Mădălin Ionel Patrașcu +;;; Copyright © 2019, 2021-2023 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Riku Viitanen ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 sirgazil @@ -2690,6 +2690,27 @@ (define-public python-diskcache (description "DiskCache is a disk and file backed persistent cache.") (license license:asl2.0))) +(define-public python-optparse-pretty + (package + (name "python-optparse-pretty") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "optparse-pretty" version)) + (sha256 + (base32 "1920wbh2b7a8qn7zx2iiqbcdaax335l81a73x9pp8h11yzs2jdmh")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f)) ; There are no tests in the pypi archive. + (home-page "https://github.com/gvalkov/optparse-pretty") + (synopsis "Compact help formatter for optparse") + (description + "This module provides two help formatters for optparse. They provide +terser and more customizable option formatting in comparison to the default +help formatter.") + (license license:bsd-3))) + (define-public python-orjson (package (name "python-orjson") From patchwork Thu May 11 18:34:12 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 49941 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 674EE27BBF0; Thu, 11 May 2023 19:35:17 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=ham 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 63F6C27BBEE for ; Thu, 11 May 2023 19:35:16 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pxB85-0003io-Ha; Thu, 11 May 2023 14:35:05 -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 1pxB84-0003iI-By for guix-patches@gnu.org; Thu, 11 May 2023 14:35:04 -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 1pxB83-0004Tp-Sz for guix-patches@gnu.org; Thu, 11 May 2023 14:35:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pxB82-0001V3-J2; Thu, 11 May 2023 14:35:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63448] [PATCH 2/2] gnu: Add python-mgatk. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Thu, 11 May 2023 18:35:02 +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> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 63448-submit@debbugs.gnu.org id=B63448.16838300855731 (code B ref 63448); Thu, 11 May 2023 18:35:02 +0000 Received: (at 63448) by debbugs.gnu.org; 11 May 2023 18:34:45 +0000 Received: from localhost ([127.0.0.1]:53349 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pxB7l-0001UM-A0 for submit@debbugs.gnu.org; Thu, 11 May 2023 14:34:45 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:37499) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pxB7k-0001Ty-0e for 63448@debbugs.gnu.org; Thu, 11 May 2023 14:34:44 -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 :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1683830077; x=1685644478; bh=5L6oq84uAxetpfl3MC1Zp5P18nKn7WnzdSusnB2aYss=; b=LgdX63CuPaeS T2Ute7GkkTiOcFCEiIjHUkhyo1btRwffZuXPtu295dcS2jYM1ttCR90mJjTTYnPY fMWQpYppbxDDmYdhx4+j8m0VboFptptKpXNrw0KrSzS1w+3ri0B3NeeBtbUUjTtk qVhiHoxLfJXXvH41euOTkFHpzdVzccM= 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 b2062.mx.srv.dfn.de (Postfix) with ESMTPS id DE7EC160171 for <63448@debbugs.gnu.org>; Thu, 11 May 2023 20:34:37 +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; Thu, 11 May 2023 20:34:36 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 11 May 2023 20:34:12 +0200 Message-ID: <20230511183412.27180-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230511183412.27180-1-madalinionel.patrascu@mdc-berlin.de> References: <20230511183412.27180-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27620.001 X-TM-AS-Result: No-10--6.127000-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2t6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt/mEPaHBc5dL3nHtGkYl/VpdSt9kxxIQniiCVsScJChxte+ ocL7MBZeKbindmE5bmHTNo9ln6uywJnRO1kR8OZ4Oy1AV8tUD8Mf3EaOZ0dNKOGo4dIdACSCYDT IhMw3OOX0tCKdnhB589yM15V5aWpj6C0ePs7A07YFInLyeDAoZ5TuGK+UjhjDzSiOla5yXDZj9B lckre/3pQcA7zQaRwnBLHK11ZlC+A== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.127000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27620.001 X-TM-SNTS-SMTP: ADE19DEA6BB6ABFFDA73B97C81379E189BDAD577A602D483223A4314832464042002: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+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 (python-mgatk): New variable. --- gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index afca5ab93b..92017b3a07 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12628,6 +12628,41 @@ (define-public python-biothings-client API services.") (license license:bsd-3))) +(define-public python-mgatk + (package + (name "python-mgatk") + (version "0.6.7") + (source + (origin + (method url-fetch) + (uri (pypi-uri "mgatk" version)) + (sha256 + (base32 "0bxxk3v8lmqcdnm97468p7p3kzb59i5bpgayx7kqzl2p8lfwzi9h")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f)) ; There are no tests in the pypi archive. + (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-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")