From patchwork Thu Feb 2 16:00:22 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 46597 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 60F6527BBE9; Thu, 2 Feb 2023 16:01:32 +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=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 2D3AD27BBED for ; Thu, 2 Feb 2023 16:01:30 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pNc1K-0004L3-N4; Thu, 02 Feb 2023 11:01:06 -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 1pNc1H-0004IG-CQ for guix-patches@gnu.org; Thu, 02 Feb 2023 11:01:03 -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 1pNc1H-0001MT-3y for guix-patches@gnu.org; Thu, 02 Feb 2023 11:01:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pNc1G-0006t3-Ue for guix-patches@gnu.org; Thu, 02 Feb 2023 11:01:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61230] [PATCH 1/2] gnu: Add python-pegasusio. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 02 Feb 2023 16:01:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61230 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61230@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.167535365026428 (code B ref -1); Thu, 02 Feb 2023 16:01:02 +0000 Received: (at submit) by debbugs.gnu.org; 2 Feb 2023 16:00:50 +0000 Received: from localhost ([127.0.0.1]:35552 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNc14-0006s6-7H for submit@debbugs.gnu.org; Thu, 02 Feb 2023 11:00:50 -0500 Received: from lists.gnu.org ([209.51.188.17]:33482) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNc12-0006rq-3o for submit@debbugs.gnu.org; Thu, 02 Feb 2023 11:00:48 -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 1pNc11-0004Es-M8 for guix-patches@gnu.org; Thu, 02 Feb 2023 11:00:47 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pNc0y-0001Cc-FC for guix-patches@gnu.org; Thu, 02 Feb 2023 11:00:47 -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=1675353641; x=1677168042; bh=VH83Q/Il85B8PVD EHCsv4VDdnh+ibUr3pH2rtmrRNE0=; b=WvtoeQmMerJBysUTyl5cnnp55f00iso toqNFq1CX2DqbC/9kEa2GlNxx63XefxXbncP2Jk7/b6IZVRYnucFp5A/0gpJ3VJH klwc6aTMlEg+mvn8yMJVMHcYQwFDQYZjOKmPaovBWbbr2+9ZO5pZX4xtOc9Hup7s k/uPSQupz5dA= 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 0E9961604D4 for ; Thu, 2 Feb 2023 17:00:41 +0100 (CET) Received: from localhost.localdomain (10.84.128.47) 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; Thu, 2 Feb 2023 17:00:35 +0100 From: Navid Afkhami Date: Thu, 2 Feb 2023 17:00:22 +0100 Message-ID: <20230202160023.45975-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [10.84.128.47] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27424.000 X-TM-AS-Result: No-10--1.107300-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXR6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VL6p xbTOjavycW3/J21vqoVXOLTjXPci/yq+GZ9ZHxIhuW77/y896sjb4QM/D7zGt0JZ5MDd4/kU5wM PMqdPNSzns4projbTGT3mnWKOM3JF5UcZtwNsCroURSScn+QSXhhJCIHRlO51+gtHj7OwNO22ut O5qEfOUXI4Nf39Ohr8tK/Zg5sgElcpl+tEyIt7+AhAiMmxd1U+EeTv/avrG+qQlI1R8BktUFk9y 0x1JyPRiyu7pv5683MOeLzJ7zyIOHQJ88ZHP8DjvmJf6uotZp79ZjtYmCyQ6k+HGwSCjLh6vuvB 6gAgryg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.107300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27424.000 X-TM-SNTS-SMTP: 2ABF608266911343DCF244D0635AF350DC8A44983652684217B58A95F500DB2F2002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.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-pegasusio): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 714db27c16..6caf0e4cfa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1136,6 +1136,36 @@ (define-public python-htsget servers supporting the protocol.") (license license:asl2.0))) +(define-public python-pegasusio + (package + (name "python-pegasusio") + (version "0.7.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pegasusio" version)) + (sha256 + (base32 + "0gqygspdy398vjymdy6756jmk99s7fhwav9rivdx59kpqjcdxaz9")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-anndata + python-docopt + python-h5py + python-importlib-metadata + python-loompy + python-natsort + python-numpy + python-pandas + python-pillow + python-scipy + python-zarr)) + (native-inputs (list python-cython python-setuptools-scm)) + (home-page "https://github.com/lilab-bcb/pegasusio") + (synopsis + "Pegasusio is a Python package for reading or writing single-cell genomics data") + (description + "Pegasusio is a Python package for reading or writing single-cell genomics data.") + (license license:bsd-3))) + (define-public python-phylophlan (package (name "python-phylophlan") From patchwork Thu Feb 2 16:00:23 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 46596 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 C2C7C27BBEB; Thu, 2 Feb 2023 16:01:31 +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=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 E7BDB27BBE9 for ; Thu, 2 Feb 2023 16:01:29 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pNc1J-0004Ig-8u; Thu, 02 Feb 2023 11:01:05 -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 1pNc1G-0004I5-Sg for guix-patches@gnu.org; Thu, 02 Feb 2023 11:01:02 -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 1pNc1G-0001M1-Iw for guix-patches@gnu.org; Thu, 02 Feb 2023 11:01:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pNc1G-0006so-7P for guix-patches@gnu.org; Thu, 02 Feb 2023 11:01:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61229] [PATCH 2/2] gnu: Add python-demuxem. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 02 Feb 2023 16:01:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61229 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61229@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.167535365026421 (code B ref -1); Thu, 02 Feb 2023 16:01:02 +0000 Received: (at submit) by debbugs.gnu.org; 2 Feb 2023 16:00:50 +0000 Received: from localhost ([127.0.0.1]:35550 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNc13-0006s4-Si for submit@debbugs.gnu.org; Thu, 02 Feb 2023 11:00:50 -0500 Received: from lists.gnu.org ([209.51.188.17]:33484) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNc12-0006rr-5P for submit@debbugs.gnu.org; Thu, 02 Feb 2023 11:00:48 -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 1pNc11-0004Eu-NV for guix-patches@gnu.org; Thu, 02 Feb 2023 11:00:47 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pNc0y-0001CZ-FO for guix-patches@gnu.org; Thu, 02 Feb 2023 11:00:47 -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=1675353640; x=1677168041; bh=5M5kJhV6y7H+hteBNJWZ1vEp7iYfMNMyizTf8viYjlc=; b=aefyvNj1pj2J eDfphXU20UhxYEnhAvlURxFL65AY4HB+rbL6Eu3bwj3LdLveE98pSpe7idcFEPew 0JPKeKlQrGdqCUHvHIlFycNsNBtQa+WlpXD2nqO6QUChIptBtmpx5Szb99Qixgtt LPIZ1x/fLeuK2n0vhidn1Npj+iSVVyg= 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 574D11604D0 for ; Thu, 2 Feb 2023 17:00:40 +0100 (CET) Received: from localhost.localdomain (10.84.128.47) 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; Thu, 2 Feb 2023 17:00:35 +0100 From: Navid Afkhami Date: Thu, 2 Feb 2023 17:00:23 +0100 Message-ID: <20230202160023.45975-2-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230202160023.45975-1-navid.afkhami@mdc-berlin.de> References: <20230202160023.45975-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [10.84.128.47] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27424.000 X-TM-AS-Result: No-10--4.814400-5.000000 X-TMASE-MatchedRID: toN6SH028bV6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXb1veicsGbWruNT8xdcEnQwE+dA3RWUSv/9mRo9wUk+WFzNNPDc6umOCbuVI7hVbLfEz RZ8UqjkrF+KCpGE37CJsoi2XrUn/Jn6KdMrRsL14qtq5d3cxkNRqXnrxrKCOXt65UhzoDutvgom dJ1Fga8Tt8/xnfxZuzquq0fsrhwY7iwNHeHzF5Ov9ENsQ2Cqm3hnTs6l8lrxvS6zpiqHFy9FgAB EzH44G0DUEkBTZ8vOLxlyTCXQR4xioA5PA4dQuxuYpJR2kheXd+3BndfXUhXQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.814400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27424.000 X-TM-SNTS-SMTP: BD2CB0AD7D46C5C08A36F9E1723CE05F1CF8DC050EA1A0E5A6AB287BD1F36BF72002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.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-demuxem): New variable. --- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6caf0e4cfa..406f8616c7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1090,6 +1090,35 @@ (define-public python-cmseq and sequence consensus.") (license license:expat))) +(define-public python-demuxem + (package + (name "python-demuxem") + (version "0.1.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "demuxEM" version)) + (sha256 + (base32 + "1bhyxqjk44bmyd26m1smapf68wyf7252kk65i27k50dd3kswgnd6")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-docopt + python-importlib-metadata + python-numpy + python-pandas + python-pegasusio + python-scikit-learn + python-scipy + python-seaborn)) + (native-inputs (list python-cython python-setuptools-scm)) + (home-page "https://github.com/lilab-bcb/demuxEM") + (synopsis + "This is a module on analyzing cell-hashing/nucleus-hashing data") + (description + "This is a module on analyzing cell-hashing/nucleus-hashing data. +It is the demultiplexing module of Pegasus, which is used by Cumulus +in demultiplexing step.") + (license license:bsd-3))) + (define-public python-hclust2 (package (name "python-hclust2")