From patchwork Fri Oct 14 22:52:17 2022 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: 43417 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 17AB527BBEA; Fri, 14 Oct 2022 23:54:34 +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=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 C59E227BBE9 for ; Fri, 14 Oct 2022 23:54:33 +0100 (BST) Received: from localhost ([::1]:54138 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ojTZY-0005kK-Ne for patchwork@mira.cbaines.net; Fri, 14 Oct 2022 18:54:32 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:35126) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ojTY7-0004mJ-4W for guix-patches@gnu.org; Fri, 14 Oct 2022 18:53:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:39874) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ojTY6-0001r2-Jo for guix-patches@gnu.org; Fri, 14 Oct 2022 18:53:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ojTY6-0004wH-FR for guix-patches@gnu.org; Fri, 14 Oct 2022 18:53:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#46946] [PATCH 1/2] gnu: Add python-bioframe. References: In-Reply-To: Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 14 Oct 2022 22:53:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46946 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <46946@debbugs.gnu.org> Received: via spool by 46946-submit@debbugs.gnu.org id=B46946.166578796218946 (code B ref 46946); Fri, 14 Oct 2022 22:53:02 +0000 Received: (at 46946) by debbugs.gnu.org; 14 Oct 2022 22:52:42 +0000 Received: from localhost ([127.0.0.1]:38949 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojTXm-0004vV-Dc for submit@debbugs.gnu.org; Fri, 14 Oct 2022 18:52:42 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:34745) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojTXk-0004vE-6Q for 46946@debbugs.gnu.org; Fri, 14 Oct 2022 18:52:40 -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=1665787949; x=1667602350; bh=VNubwo+Xvi9VUxz INocRedig5uaS5+54LZi/cuX+Xjg=; b=oH6hp+xPlvgWshspzwEtQQek3OpovZy Qj/Gx/ztTr+DItg8MRJSePZO817OKvZocw6ktgA5xg+Dzkn80vMxmAtEb/lfiqps uuIpMniVmY+cUtz2uHqc/cb5+QtvyTdavlQ1QxQ6Or0iCU/YpJzmi+vR6MYwjVIz HXSsjootgnpA= 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 98E30160380 for <46946@debbugs.gnu.org>; Sat, 15 Oct 2022 00:52:29 +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 15.1.2507.12; Sat, 15 Oct 2022 00:52:28 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 15 Oct 2022 00:52:17 +0200 Message-ID: <20221014225218.13626-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27202.003 X-TM-AS-Result: No-10--2.388200-5.000000 X-TMASE-MatchedRID: huMMtcahIlCaVzGETDUtnAgqYHjJNWHeKQNhMboqZlrAuQ0xDMaXkH4q tYI9sRE/jqQ82yy1I7Tbx4dhxASC6J5l5tqvE/eVa87CDXaKRVIxVUWGXs3C8ydEcnIP1FQIOki GGidO7I/ZyfBL0WvJF7edLpfvchkD9bPHgjnnomBIK2DGByysyl7OZ6hrwwnz/gMNehoKqTvtJx 2nLZkrAtTGCputosAbzpa5NzPyAzx9CsAh4VAyKc3WPbtc5QfmBPY4SegK3jwDBQ+XBh4YJfzxf g6IZlFlX/YMDN55TesSU447Pck+mKPFjJEFr+olwXCBO/GKkVr3FLeZXNZS4DXnYt5w4ccjgHXF 9sw5Dnqy84sUa/Axm81gddartF+2hgYnLsv5sqGlRrAhf46dQKRBf4r1DclnVh09B9JWceM9kGB keUdHfKegIxa0HvgjjztWiTRPtkUKGB9MbH1S7rTnVnv1JP77sGTvZJmllrz/PhPL0kApH8kjm+ elEcbI X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.388200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27202.003 X-TM-SNTS-SMTP: 0D36357AE3EF053C29DC01A66A6BD6BEF018BA011D27D47D322CCBD87A8D6CA42002: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" X-getmail-retrieved-from-mailbox: Patches X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioinformatics.scm (python-bioframe): New variable. --- gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) base-commit: 10d429f2fce321d8285684503094694ec3979865 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f2de09aa32..1478ba0c46 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -946,6 +946,52 @@ (define (cythonized? c/c++-file) ;; licensed lgpl2.1+ (license (list license:expat license:lgpl2.1+)))) +(define-public python-bioframe + (package + (name "python-bioframe") + (version "0.3.3") + (source + (origin + (method git-fetch) + ;; pypi version does not contain tests and requirements.txt + (uri (git-reference + (url "https://github.com/open2c/bioframe") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "14lvb18d4npapyi6j2zqh9q94l658dzmka5riiizw1h0zb0kp9xb")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (setenv "MPLCONFIGDIR" "/tmp") + (when tests? + (invoke "pytest" "-v"))))))) + (native-inputs + (list python-biopython + python-pysam + python-pytest + python-wheel)) + (propagated-inputs + (list python-matplotlib + python-numpy + python-pandas + python-requests)) + (home-page "https://github.com/open2c/bioframe") + (synopsis "Pandas utilities for tab-delimited and other genomic files") + (description + "This package is a library to enable flexible and scalable operations on +genomic interval dataframes in @code{python}. @code{python-bioframe} enables +access to a rich set of dataframe operations. Working in @code{python} enables +rapid visualization (e.g. @code{matplotlib}, @code{seaborn}) and iteration of +genomic analyses. The philosophy underlying @code{python-bioframe} is to enable +flexible operations. Instead of creating a function for every possible use-case, +we encourage users to compose functions to achieve their goals.") + (license license:expat))) + (define-public python-biom-format (package (name "python-biom-format") From patchwork Fri Oct 14 22:52:18 2022 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: 43416 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 7220027BBEA; Fri, 14 Oct 2022 23:53:16 +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=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 2997927BBE9 for ; Fri, 14 Oct 2022 23:53:16 +0100 (BST) Received: from localhost ([::1]:51340 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ojTYI-0004qA-9s for patchwork@mira.cbaines.net; Fri, 14 Oct 2022 18:53:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:35128) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ojTY7-0004nI-8c for guix-patches@gnu.org; Fri, 14 Oct 2022 18:53:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:39875) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ojTY7-0001r9-0b for guix-patches@gnu.org; Fri, 14 Oct 2022 18:53:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ojTY6-0004wP-SO for guix-patches@gnu.org; Fri, 14 Oct 2022 18:53:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#46946] [PATCH 2/2] gnu: Add python-cooltools. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 14 Oct 2022 22:53:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46946 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <46946@debbugs.gnu.org> Received: via spool by 46946-submit@debbugs.gnu.org id=B46946.166578796618960 (code B ref 46946); Fri, 14 Oct 2022 22:53:02 +0000 Received: (at 46946) by debbugs.gnu.org; 14 Oct 2022 22:52:46 +0000 Received: from localhost ([127.0.0.1]:38952 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojTXp-0004vk-Qv for submit@debbugs.gnu.org; Fri, 14 Oct 2022 18:52:46 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:37813) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojTXn-0004vL-Sx for 46946@debbugs.gnu.org; Fri, 14 Oct 2022 18:52:44 -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=1665787954; x=1667602355; bh=wX7DPjmBxpmrDG5INvusUAsBUceM5Wb6qoaBMqf07tM=; b=kVib4pJzFKbJ WwVAYMPcWmMgCMhs9/0AIrNPj7Pojcq+PQqH53PhodtSLiQzL0D/13gpIOzFUfGX nlzBH0EF8+KGoy7K9kYVz1fM8kIMmGevU+yX9NDXREHwdDZzeMHuLn+ag1BO0k9n jWrBqon4vIWx2nfa1dx1qvXzgsjdj/c= 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 1036816039C for <46946@debbugs.gnu.org>; Sat, 15 Oct 2022 00:52:34 +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 15.1.2507.12; Sat, 15 Oct 2022 00:52:28 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 15 Oct 2022 00:52:18 +0200 Message-ID: <20221014225218.13626-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 In-Reply-To: <20221014225218.13626-1-madalinionel.patrascu@mdc-berlin.de> References: <20221014225218.13626-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27202.003 X-TM-AS-Result: No-10--3.679100-5.000000 X-TMASE-MatchedRID: NGDYxnKYxb2aVzGETDUtnAgqYHjJNWHeKQNhMboqZlrAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvutvHF25zoU9hXC3lnHCTmdW0pkpPR1DaOXf Z9OHyzWabOWTHQMIg6+Qw/NrlqdZPO5k/PxBAvv6+vuhCHYf16675nIWq13kVQlnkwN3j+RSETM jf6aTOJ8/NOC9mefryF/q6px2NM/mhznSgFQVXH6ubsOtSWY2QgDLqnrRlXrZ8nn9tnqel2MprJ P8FBOIaJIVnHAEf5ZGsT8k1Ey2W3geiuHcJRjyZ+LZxR9gx6EFcZ97q3zV+t4vS025qqeCRs2fA TIQH5n3yLHvZd0qf3Pfo+7Q5y5vLu9e6mwL34S+051Z79ST++7Bk72SZpZa8/z4Ty9JAKR/JI5v npRHGyA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.679100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27202.003 X-TM-SNTS-SMTP: 2881F355960ABEBE15BD112E3518B3697809FD88AD62AF31DF0A0729295FD2642002: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" X-getmail-retrieved-from-mailbox: Patches X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioinformatics.scm (python-cooltools): New variable. --- gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1478ba0c46..6f228fb907 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12977,6 +12977,51 @@ (define-public python-cooler such as Hi-C contact matrices.") (license license:bsd-3))) +(define-public python-cooltools + (package + (name "python-cooltools") + (version "0.5.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "cooltools" version)) + (sha256 + (base32 + "08hyzd3kazr87nvv6rwp5i1g9rwj7jmrly925lqnvippz4wp7k4g")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (setenv "MPLCONFIGDIR" "/tmp") + (when tests? + (invoke "pytest" "-v"))))))) + (native-inputs + (list python-cython + python-pytest)) + (propagated-inputs + (list python-bioframe + python-click + python-cooler + python-joblib + python-matplotlib + python-multiprocess + python-numba + python-numpy + python-pandas + python-scikit-image + python-scikit-learn + python-scipy)) + (home-page "https://github.com/open2c/cooltools") + (synopsis + "Analysis tools for genomic interaction data stored in .cool format") + (description + "This package provides necessary tools for the analysis of the genomic +interaction data stored in @code{.cool} format. This collection of tools includes +operations like compartment, insulation or peak calling.") + (license license:expat))) + (define-public python-hicmatrix (package (name "python-hicmatrix")