From patchwork Sun Jan 22 00:49:48 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: 46329 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 258AC27BBED; Sun, 22 Jan 2023 00:51:33 +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=-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=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 4D3DE27BBE9 for ; Sun, 22 Jan 2023 00:51:31 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pJOZe-0001bY-F2; Sat, 21 Jan 2023 19:51:06 -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 1pJOZb-0001aV-Ew for guix-patches@gnu.org; Sat, 21 Jan 2023 19:51:04 -0500 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 1pJOZb-0004yN-6Q for guix-patches@gnu.org; Sat, 21 Jan 2023 19:51:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pJOZb-0000jA-21; Sat, 21 Jan 2023 19:51:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60997] [PATCH 1/4] gnu: Add python-cmseq. References: <55c300694f6c49f6a89a8018a3f86729@mdc-berlin.de> In-Reply-To: <55c300694f6c49f6a89a8018a3f86729@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: Sun, 22 Jan 2023 00:51:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60997 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <60997@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 60997-submit@debbugs.gnu.org id=B60997.16743486182720 (code B ref 60997); Sun, 22 Jan 2023 00:51:03 +0000 Received: (at 60997) by debbugs.gnu.org; 22 Jan 2023 00:50:18 +0000 Received: from localhost ([127.0.0.1]:50100 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pJOYr-0000hi-KW for submit@debbugs.gnu.org; Sat, 21 Jan 2023 19:50:18 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:47885) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pJOYp-0000h0-9i for 60997@debbugs.gnu.org; Sat, 21 Jan 2023 19:50:15 -0500 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=1674348609; x=1676163010; bh=aFSdvXn0nFcHHkr hqtDI75RkRJKDMpr1XT2R4cPasK8=; b=qUsPIrqbrCzDXN3/AAMvUe//F2A39Ib ZHSo1eZAvIMUhyUnuTvAGQNmZjUqdj4wmm400fdqfQN4OLNhYbfaGtFNDacdEMA+ UqyoEoCoPH+TLBuFv5BDUQR4P8t315+teMwV3LXBDL2tbpX6ipHnFxMxZ/3HoGih puX0GVsZDq/g= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 2D5F430062B for <60997@debbugs.gnu.org>; Sun, 22 Jan 2023 01:50:09 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Sun, 22 Jan 2023 01:50:02 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sun, 22 Jan 2023 01:49:48 +0100 Message-ID: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27400.003 X-TM-AS-Result: No-10--4.099000-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2t6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaLVSacMk7Gpjk00j3lQv+fSq+GZ9ZHxIhuW77/y896sgxVUWGXs3C80JZ5MDd4/kU7Fo gUQ0vV9jUxgqbraLAG9Uf8/gZ0Wa4QZkWVkqJ8k7jpxdo/JwVm7+a+v4FF31u4UCO0g9+SWbX7Q qxdrFbPufOVcxjDhcwWWZjCFLCEBoLbigRnpKlKTpcQTtiHDgWFoIgbDV0aSMKHkPMR6/bMpp3T L9efcte4gRtrw7AjA555Qn7UOW874aV5yzrZhTXYTtDyfkcZbPrKN/TUXSiFBZPemFmky/i3yJq 1ESN+kMTydv0PB1DgLaNtJpvWmDRSPEWnCfndI5+GPkJmSZLIg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.099000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27400.003 X-TM-SNTS-SMTP: A016B8B2094F8560FEDAECA4BF72F77A034A2E832A7D531F2BFF07F1A80BC6F32002: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-cmseq): New variable. --- gnu/packages/bioinformatics.scm | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) base-commit: f088763356e88c4911ee933fdafcad6ed66a7aa3 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 36c9db90bd..4e7bc07a5f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2017, 2021, 2022 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits -;;; Copyright © 2018, 2019, 2020, 2021, 2022 Mădălin Ionel Patrașcu +;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu ;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio @@ -1014,6 +1014,33 @@ (define-public python-cellbender from high-throughput single-cell RNA sequencing (scRNA-seq) data.") (license license:bsd-3))) +(define-public python-cmseq + (package + (name "python-cmseq") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "CMSeq" version)) + (sha256 + (base32 + "0p6a99c299m5wi2z57dgqz52m1z3nfr8mv7kdnk2jvl2p9nql0wk")))) + (build-system python-build-system) + (arguments + (list #:tests? #f )) ;pypi no tests + (propagated-inputs + (list python-bcbio-gff + python-biopython + python-numpy + python-pandas + python-pysam + python-scipy)) + (home-page "http://github.com/SegataLab/cmseq/") + (synopsis "Set of utilities on sequences and BAM files") + (description + "CMSeq is a set of commands to provide an interface to .bam files for coverage +and sequence consensus.") + (license license:expat))) + (define-public python-htsget (package (name "python-htsget") From patchwork Sun Jan 22 00:49:49 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: 46330 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 5EBD027BBF1; Sun, 22 Jan 2023 00:51:31 +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=-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 0F9B227BBED for ; Sun, 22 Jan 2023 00:51:29 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pJOZf-0001be-1F; Sat, 21 Jan 2023 19:51:07 -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 1pJOZa-0001aR-T1 for guix-patches@gnu.org; Sat, 21 Jan 2023 19:51:04 -0500 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 1pJOZa-0004vc-Kw for guix-patches@gnu.org; Sat, 21 Jan 2023 19:51:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pJOZa-0000it-6m; Sat, 21 Jan 2023 19:51:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60997] [PATCH 2/4] gnu: Add python-hclust2. 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: Sun, 22 Jan 2023 00:51:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60997 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <60997@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 60997-submit@debbugs.gnu.org id=B60997.16743486172700 (code B ref 60997); Sun, 22 Jan 2023 00:51:02 +0000 Received: (at 60997) by debbugs.gnu.org; 22 Jan 2023 00:50:17 +0000 Received: from localhost ([127.0.0.1]:50096 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pJOYq-0000hT-LU for submit@debbugs.gnu.org; Sat, 21 Jan 2023 19:50:17 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:49549) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pJOYo-0000gz-Kg for 60997@debbugs.gnu.org; Sat, 21 Jan 2023 19:50:15 -0500 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=1674348608; x=1676163009; bh=Nf6oksiBeSGVK65NQcG5M7yDIfZOUxOS/pEoJbcVVS8=; b=N0kFygMJ4l++ sla8nzcqgK8bUX/U5eYYGYLYAJk5MsbSE8jh5d9BefRhiEEgcVGqhQHL6y1JmcqO 1IyqOTbuNBk+kq5NGpkoerfYeXtPuWeyIYlxW/ZOF1e6UJDLr/SUzXzRY36qHRf8 ZmKcWS7ghoxT9jt3ugE6XyDGnjRX5Yc= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 6A428300627 for <60997@debbugs.gnu.org>; Sun, 22 Jan 2023 01:50:08 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Sun, 22 Jan 2023 01:50:02 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sun, 22 Jan 2023 01:49:49 +0100 Message-ID: <20230122004951.119277-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de> References: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27400.003 X-TM-AS-Result: No-10--5.081200-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXb1veicsGbWruNT8xdcEnQwE+dA3RWUSvutvHF25zoU8xVUWGXs3C80JZ5MDd4/kUssb EkSX6c0kV5MniPWJBrU0Tjw561BCIxVDWOuzmzZI7lKkz03w0630tCKdnhB58I/9UW5M5dRMQpr Z/7WnuveTCMddcL/gjymsk/wUE4hpau/Gkfjk+cHaPMzQ1g8/CmQ7rVt1ovvbgrZu5D215bUzVm 4+JPhSp X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.081200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27400.003 X-TM-SNTS-SMTP: 188361D524DE3ED5CF3B060DA68204EA61453ED706E4BB700AC99525AA82BC6C2002: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-hclust2): New variable. --- gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4e7bc07a5f..bf01c9c7e4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1041,6 +1041,32 @@ (define-public python-cmseq and sequence consensus.") (license license:expat))) +(define-public python-hclust2 + (package + (name "python-hclust2") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "hclust2" version)) + (sha256 + (base32 + "0v89n2g42d7jhgfs8glf06apgxx6aswp3mfisgnhm518cv8z2rwn")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f)) ;;pypi no tests + (propagated-inputs + (list python-matplotlib + python-numpy + python-pandas + python-scipy)) + (home-page "http://github.com/SegataLab/hclust2/") + (synopsis "Plotting heat-maps for publications") + (description + "Hclust2 is a handy tool for plotting heat-maps with several useful options +to produce high quality figures that can be used in publication") + (license license:expat))) + (define-public python-htsget (package (name "python-htsget") From patchwork Sun Jan 22 00:49:50 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: 46331 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 DA5DC27BBEB; Sun, 22 Jan 2023 00:51:40 +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=-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=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 F291627BBE9 for ; Sun, 22 Jan 2023 00:51:39 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pJOZe-0001bM-7z; Sat, 21 Jan 2023 19:51:06 -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 1pJOZc-0001aa-0v for guix-patches@gnu.org; Sat, 21 Jan 2023 19:51:05 -0500 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 1pJOZb-000520-PT for guix-patches@gnu.org; Sat, 21 Jan 2023 19:51:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pJOZb-0000jJ-Gp; Sat, 21 Jan 2023 19:51:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60997] [PATCH 3/4] gnu: Add python-phylophlan. 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: Sun, 22 Jan 2023 00:51:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60997 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <60997@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 60997-submit@debbugs.gnu.org id=B60997.16743486262735 (code B ref 60997); Sun, 22 Jan 2023 00:51:03 +0000 Received: (at 60997) by debbugs.gnu.org; 22 Jan 2023 00:50:26 +0000 Received: from localhost ([127.0.0.1]:50102 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pJOZ0-0000i3-6d for submit@debbugs.gnu.org; Sat, 21 Jan 2023 19:50:26 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:56973) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pJOYq-0000h4-GN for 60997@debbugs.gnu.org; Sat, 21 Jan 2023 19:50:17 -0500 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=1674348610; x=1676163011; bh=nu75s7w1NREC84OHk+v3wWBhktIzcIlYYetqWP6THS4=; b=JLWGie+QBGNo K92YbzHxWvlxV1d1bJP22LW7yjuVyiEp1WuSah0GtLynj+IECS/6yW9zKccvJ9ae WMo4U0uVH4RA6lWwvDYqAVWv6cnub/nXtM9hLVNmVYJ6ylxJUnO6iGpuz+QOPjxw PBpuEcKz2l/XDWgAaTMFuRVChN2xOWk= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id E9ED030062F for <60997@debbugs.gnu.org>; Sun, 22 Jan 2023 01:50:09 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Sun, 22 Jan 2023 01:50:02 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sun, 22 Jan 2023 01:49:50 +0100 Message-ID: <20230122004951.119277-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de> References: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27400.003 X-TM-AS-Result: No-10--1.305800-5.000000 X-TMASE-MatchedRID: cSoPLjBYd516fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VL6p xbTOjavycW3/J21vqoVXOLTjXPci/yq+GZ9ZHxIhuW77/y896sj4uJ1REX4MHYwnGKAoIKJLEOE Te7tkwKLjAPlvErk6O9FXyRPnllrtJVWqk0NljVzX3j/lf1V8LIXM008Nzq6YEd+K6O5Nt516Ir AOmyMThC3t+29FTIl+KRv0QBIBWgfx/7riAssTAmlO3nte6oxzFLc12YGVrZCBbptjxI6rdaPFj JEFr+olwXCBO/GKkVr3FLeZXNZS4CiM3WUt6LtFRN2XbKA3/DFnFkJnoSEcYEXNQ/bM3ourxa4y Joju5AqBLcYgS77e4a0YfXj3xoyv95Z7qptePZo1gjbDk5pb3TjLNIuhsPMtWSgmpbFZnEI1kD2 KtSTmq2Pbt5Stv2K5/Ox0TU9Ci5I= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.305800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27400.003 X-TM-SNTS-SMTP: F92D2136B323028728C5F140C07FEE12B88FA64189834706127D85D0BA08C12E2002: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-phylophlan): New variable. --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bf01c9c7e4..5c9c222d59 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1089,6 +1089,49 @@ (define-public python-htsget servers supporting the protocol.") (license license:asl2.0))) +(define-public python-phylophlan + (package + (name "python-phylophlan") + (version "3.0.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "PhyloPhlAn" version)) + (sha256 + (base32 + "1r1bnnh4d38l410hfzf882y43ln8fd2lcsqbralqshxqw2hzc7x7")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f ;pypi no tests + #:phases + #~(modify-phases %standard-phases + ;;pypi does not provide the readme.md file + (add-before 'build 'loose-readme-file-requirement + (lambda _ + (substitute* "setup.py" + (("long_description") + "#long_description"))))))) + (propagated-inputs + (list python-biopython + python-dendropy + python-matplotlib + python-numpy + python-pandas + python-seaborn)) + (home-page "https://github.com/biobakery/phylophlan") + (synopsis + "Phylogenetic analysis of microbial isolates and genomes from metagenomes") + (description + "This package is an integrated pipeline for large-scale phylogenetic profiling +of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use +method for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. This software package can assign both genomes +and @acronym{MAGs, metagenome-assembled genomes} to @acronym{SGBs, species-level +genome bins}. PhyloPhlAn can reconstruct strain-level phylogenies using clade- +specific maximally informative phylogenetic markers, and can also scale to very +large phylogenies comprising >17,000 microbial species.") + (license license:expat))) + (define-public python-pybedtools (package (name "python-pybedtools") From patchwork Sun Jan 22 00:49:51 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: 46328 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 8F4D027BBF0; Sun, 22 Jan 2023 00:51:30 +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=-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 AF7EE27BBE9 for ; Sun, 22 Jan 2023 00:51:26 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pJOZe-0001bd-NN; Sat, 21 Jan 2023 19:51:06 -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 1pJOZb-0001aU-BN for guix-patches@gnu.org; Sat, 21 Jan 2023 19:51:04 -0500 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 1pJOZa-0004xU-Nq for guix-patches@gnu.org; Sat, 21 Jan 2023 19:51:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pJOZa-0000j2-KQ; Sat, 21 Jan 2023 19:51:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60997] [PATCH 4/4] gnu: Add python-metaphlan. 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: Sun, 22 Jan 2023 00:51:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60997 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <60997@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 60997-submit@debbugs.gnu.org id=B60997.16743486172713 (code B ref 60997); Sun, 22 Jan 2023 00:51:02 +0000 Received: (at 60997) by debbugs.gnu.org; 22 Jan 2023 00:50:17 +0000 Received: from localhost ([127.0.0.1]:50098 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pJOYr-0000hV-4F for submit@debbugs.gnu.org; Sat, 21 Jan 2023 19:50:17 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:57605) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pJOYo-0000gx-Kc for 60997@debbugs.gnu.org; Sat, 21 Jan 2023 19:50:15 -0500 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=1674348607; x=1676163008; bh=93Va/WOHl4jTS8nl/bR+WJafNJjUZIdPKsTI2m4x0kQ=; b=hmG1aW8eHibX s0u833IGsVhdo3lsqIJEe07TRXO8EtzPETQR7pSKRxebhErjwcHq6Qjaozjl2z+c 5XNI6VqYI5cG90SKbZiIqIOskWZ3wFvOREO/5C5ZA8gZLq+S0JoNELgauw1aNUVB somv9GOofgergXrhX8V4dJCTxUq1cIQ= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 636D630061F for <60997@debbugs.gnu.org>; Sun, 22 Jan 2023 01:50:07 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Sun, 22 Jan 2023 01:50:02 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sun, 22 Jan 2023 01:49:51 +0100 Message-ID: <20230122004951.119277-4-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de> References: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27400.003 X-TM-AS-Result: No-10--0.003900-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt0fr6WG4Th9aPKN38CLPK0HjLrHqvAiSy0JZ5MDd4/kUssb EkSX6c0kV5MniPWJBrfBilazGYLz48f+64gLLEwLdCok3ibXlQX0tCKdnhB58I/9UW5M5dRMFaB V3gxX49eTCMddcL/gjymsk/wUE4ho/O6OLhVHRUUcQiBHaPZfP8ncxpUcsJvpEPHtsX1N/My1vt GHpizXfZBU2u/t2CWcAGScLyx0UEyPumN1GtN28Bt/pnRZkhbY12HPnv77W17TnVnv1JP77sGTv ZJmllrz/PhPL0kApH8kjm+elEcbI X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.003900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27400.003 X-TM-SNTS-SMTP: AC02B7398F7A5986B19A0637128EF6EA0765B186C1ED1AF69A085C6147C2D7052002: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-metaphlan): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5c9c222d59..884e5aa1e5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11234,6 +11234,43 @@ (define-public python-biothings-client API services.") (license license:bsd-3))) +(define-public python-metaphlan + (package + (name "python-metaphlan") + (version "4.0.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "MetaPhlAn" version)) + (sha256 + (base32 + "1jw29m8p8bcwn4q5qvh8s96qlgqv1kaizbmm87jk55f34k1y3y8a")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f)) ;pypi no tests + (propagated-inputs + (list python-biom-format + python-biopython + python-cmseq + python-dendropy + python-h5py + python-hclust2 + python-numpy + python-pandas + python-phylophlan + python-pysam + python-requests + python-scipy)) + (home-page "http://github.com/biobakery/MetaPhlAn/") + (synopsis "Metagenomic phylogenetic analysis") + (description + "MetaPhlAn is a computational tool for profiling the composition of microbial +communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing +data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, +it is now possible to perform accurate strain-level microbial profiling.") + (license license:expat))) + (define-public python-multivelo (package (name "python-multivelo")