From patchwork Fri Dec 16 16:01:15 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 45378 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 13FD527BBE9; Fri, 16 Dec 2022 16:03:32 +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 A5A8127BBEB for ; Fri, 16 Dec 2022 16:03:28 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p6DAu-0006KW-KB; Fri, 16 Dec 2022 11:03:04 -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 1p6DAt-0006IH-2H for guix-patches@gnu.org; Fri, 16 Dec 2022 11:03:03 -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 1p6DAs-0002lS-QB for guix-patches@gnu.org; Fri, 16 Dec 2022 11:03:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p6DAs-0001Fa-48 for guix-patches@gnu.org; Fri, 16 Dec 2022 11:03:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60124] [PATCH] gnu: Add python-bamnostic. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 16 Dec 2022 16:03:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 60124 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 60124@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16712065214779 (code B ref -1); Fri, 16 Dec 2022 16:03:01 +0000 Received: (at submit) by debbugs.gnu.org; 16 Dec 2022 16:02:01 +0000 Received: from localhost ([127.0.0.1]:50174 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p6D9t-0001Ex-7O for submit@debbugs.gnu.org; Fri, 16 Dec 2022 11:02:01 -0500 Received: from lists.gnu.org ([209.51.188.17]:52308) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p6D9o-0001Er-0Q for submit@debbugs.gnu.org; Fri, 16 Dec 2022 11:01:59 -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 1p6D9l-0005iA-Iu for guix-patches@gnu.org; Fri, 16 Dec 2022 11:01:54 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p6D9j-0002Rj-7h for guix-patches@gnu.org; Fri, 16 Dec 2022 11:01:53 -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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1671206498; x=1673020899; bh=OlZTJ5hoBTDrrsK NN5j+Jny0Ldj8wVjqTCkh7Ew7eEo=; b=JRfmebtxMFJGcy0+HYPZuwBrvye+DJx qg5wZGnIuTEhhh04FAkIPatpvwdBoLaVj9K75YBK1T1ZnNuwuptCAIqaCh7ScyR9 H2n0RKyMuyXfLBJ+7l98RHyxZAe/4fud5Fnt8vQ/Uq5104jhZ6iAgssTMSzEyGJO Cfm2YwWG68Nw= 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 2D3F0A0146 for ; Fri, 16 Dec 2022 17:01:37 +0100 (CET) Received: from localhost.localdomain (10.84.128.34) 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 15.1.2507.16; Fri, 16 Dec 2022 17:01:37 +0100 From: Navid Afkhami Date: Fri, 16 Dec 2022 17:01:15 +0100 Message-ID: <20221216160115.32252-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [10.84.128.34] 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-14.0.0.3092-9.0.1002-27328.001 X-TM-AS-Result: No-10-0.545700-5.000000 X-TMASE-MatchedRID: cSoPLjBYd516fjezFKxXHDLRY601LrakKQNhMboqZlrAuQ0xDMaXkH4q tYI9sRE/rXMOxnDE+MQEHMLDXTawgZT6aKfZ6tn9a87CDXaKRVJITEcvqjcF4EJZ5MDd4/kU5wM PMqdPNSxHk/ClfTChpsn9hyrFbRSzoGg41PayguS628cXbnOhTzFVRYZezcLzTKLVP0BSBRvC1R bOIHkz7jt8E1FvI1h+4Et5Gj8zabtZBoF+Mb84wd0KiTeJteVB64sVlliWKx8fE8yM4pjsDxZ4y lU2GwzAxEHRux+uk8jfhP1xgyx3DK+LgRXLRKClrgnhXEVX2f8tPk/pSmfXSUY0638r5CK0CW3j 6p5/oZ8Hs/BUu3wTFzX88pf+NWNiJ3aC10Vxn4mFkTkMqydD5NxSR7be7fnTFTs4ljtt094P2K/ +wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.545700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27328.001 X-TM-SNTS-SMTP: 07B0998BD43493BDEC725EE45FB2F014D9D86253B42877A31604E9530C94029B2002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action 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-bamnostic): New variable. --- gnu/packages/bioinformatics.scm | 72 +++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e8da00d805..cb423312a8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3646,6 +3646,78 @@ (define-public edirect-go-programs go-golang-org-x-image go-golang-org-x-text)))) +(define-public python-bamnostic + (package + (name "python-bamnostic") + (version "1.1.8") + (source (origin + (method url-fetch) + (uri (pypi-uri "bamnostic" version)) + (sha256 + (base32 + "0cjpzyqz6r4lmiwry2gcxdczwpkhl3lyyjg4s8addln17691ysxk")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-pytest)) + (home-page "https://github.com/betteridiot/bamnostic/") + (synopsis + "A tool for binary alignment map, random access and parsing") + (description + "A tool for binary alignment map, random access and parsing.") + (license license:bsd-3))) + +(define-public python-episcanpy + (package + (name "python-episcanpy") + (version "0.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "episcanpy" version)) + (sha256 + (base32 + "1qqcyhyzy6idpjmidfdpzwk02hbxm25rymz42h51nlk0vd4r2wwm")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #f + #:phases + '(modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-anndata + python-bamnostic + python-h5py + python-intervaltree + python-joblib + python-kneed + python-legacy-api-wrap + python-matplotlib + python-natsort + python-networkx + python-numba + python-numpy + python-packaging + python-pandas + python-scanpy + python-scikit-learn + python-scipy + python-seaborn + python-setuptools-scm + python-statsmodels + python-tqdm + python-pysam + python-pytest + python-tbb + python-umap-learn)) + (native-inputs (list python-pytest)) + (home-page "http://github.com/colomemaria/epiScanpy") + (synopsis "A tool for epigenomics single cell analysis") + (description + "A toolkit to analyse single-cell open chromatin +and single-cell DNA methylation data.") + (license license:bsd-3))) + (define-public exonerate (package (name "exonerate")