From patchwork Fri Mar 5 14:19:30 2021 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: 27458 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 2E12927BC50; Fri, 5 Mar 2021 14:21:10 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 709F127BC4F for ; Fri, 5 Mar 2021 14:21:09 +0000 (GMT) Received: from localhost ([::1]:49966 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lIBKG-0007n4-NA for patchwork@mira.cbaines.net; Fri, 05 Mar 2021 09:21:08 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:44784) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lIBKA-0007m1-L2 for guix-patches@gnu.org; Fri, 05 Mar 2021 09:21:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:50024) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lIBKA-0002M3-9J for guix-patches@gnu.org; Fri, 05 Mar 2021 09:21:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lIBKA-0008R1-5O for guix-patches@gnu.org; Fri, 05 Mar 2021 09:21:02 -0500 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, 05 Mar 2021 14:21:02 +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> Cc: rekado@elephly.net, =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmE=?= =?utf-8?b?yJljdQ==?= Received: via spool by 46946-submit@debbugs.gnu.org id=B46946.161495402232346 (code B ref 46946); Fri, 05 Mar 2021 14:21:02 +0000 Received: (at 46946) by debbugs.gnu.org; 5 Mar 2021 14:20:22 +0000 Received: from localhost ([127.0.0.1]:33337 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lIBJW-0008Pe-0X for submit@debbugs.gnu.org; Fri, 05 Mar 2021 09:20:22 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:51215) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lIBJU-0008PN-0z for 46946@debbugs.gnu.org; Fri, 05 Mar 2021 09:20:20 -0500 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id E049BA00FB; Fri, 5 Mar 2021 15:20:13 +0100 (CET) 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:received:received; s=mdc; t= 1614954013; x=1616768414; bh=mVzSy73pohHl6zrV+tNB01c8HLLVSVol0uI e+3Gd9uo=; b=TUe51Sel2wRE2sSjLp3+UhrRp/uu+tSL4Fp8CYumZweTZxgsewb jwi8jOIYnQswI7gMIk7C6RJsAKJFyVlNW8gjuBpEqwDm5W/KlECMWFxRnLS2NRFo rmuGGZ7jzQsqlj+Ut6y1ng9Se9StCIEz5HpP1qSRqaq/JmQT1TsWBTPI= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 7vE_eJM9p4CL; Fri, 5 Mar 2021 15:20:13 +0100 (CET) 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; Fri, 5 Mar 2021 15:20:13 +0100 (CET) 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 15.1.2176.2; Fri, 5 Mar 2021 15:20:13 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 5 Mar 2021 15:19:30 +0100 Message-ID: <20210305141930.28787-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210305141930.28787-1-madalinionel.patrascu@mdc-berlin.de> References: <20210305141930.28787-1-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-14.0.0.3080-8.6.1012-26010.007 X-TM-AS-Result: No-10--3.117800-8.000000 X-TMASE-MatchedRID: TYP229Ekev4saaYlMvaOHAPZZctd3P4BRWl9Bl0RPNaH4I6QZJ07keR3 7ySpIkGCOOIn5zbTcyw5gHVxu2yZ5tsJuFUx3wevfOaYwP8dcX7IEQTlh1/QMcgVyTd/p+/Iksg phu0+71BiN1Woi4uYp+pGJSAHQICsyL4SsacYXAO+vuhCHYf16wsE9gx+4jJudroFpVy5w+lFS8 Sy/IDc9G4xLhk/yLgSD7OFUBidaqL4515TanER7FS0U/rncMc4GvHEXpfoEJx6wGV3uXm3apgNM iEzDc45fS0Ip2eEHnz3IzXlXlpamPoLR4+zsDTttrrTuahHzlHbQHDI1WXCIoq800SCYZKNPc8F 00n3OBIJYpLRbF14YQR0T0a3wTZcdLYxms+5aUeJ+qRT860nriFFQEBVOI2U4CC8wZh6tHpvx+y 4SCozttG1pfB9ENkTtDC+Oypvl/RGDgEFwm6aoD6Qrn3xh/cy X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.117800-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26010.007 X-TM-SNTS-SMTP: 2D7C018D3966EBF7844CF33C1FE6744187A079E7EC07657B08508D608F8D53292000: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 * 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 fb357b8b6c..a6ea8f831d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13652,6 +13652,51 @@ storage format, called @code{cool}, used to store genomic interaction data, such as Hi-C contact matrices.") (license license:bsd-3))) +(define-public python-cooltools +;;pypi sources requiere bioframe<0.1 while github latest version requires +;; bioframe>=0.1.0 + (let ((revision "1") + (commit "53ce4fc11d046e84ca36f3591e9e5d548de9f7b2")) + (package + (name "python-cooltools") + (version (git-version "0.3.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/open2c/cooltools") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0y1wf7a0by2kih2iy5xrwzdgw1i24cwigfz4352aq5npxrpjvj6q")))) + (build-system python-build-system) + (propagated-inputs + `(("python-bioframe" ,python-bioframe) + ("python-click" ,python-click) + ("python-cooler" ,python-cooler) + ("python-cytoolz" ,python-cytoolz) + ("python-joblib" ,python-joblib) + ("python-matplotlib" ,python-matplotlib) + ("python-multiprocess" ,python-multiprocess) + ("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy) + ("python-tables" ,python-tables))) + (native-inputs + `(("python-cython" ,python-cython))) + (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 .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")