Ricardo Wurmus <rekado@HIDDEN>
to control <at> debbugs.gnu.org
.
Full text available.Received: (at 60997) by debbugs.gnu.org; 24 Jan 2023 09:15:40 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Jan 24 04:15:39 2023 Received: from localhost ([127.0.0.1]:55856 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1pKFP1-00040f-LG for submit <at> debbugs.gnu.org; Tue, 24 Jan 2023 04:15:39 -0500 Received: from sender3-of-o58.zoho.com ([136.143.184.58]:21811) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1pKFOz-00040S-4W; Tue, 24 Jan 2023 04:15:38 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1674551734; cv=none; d=zohomail.com; s=zohoarc; b=jqr1cep3TfY9CaxmEJpE1ICFX792ypf0rgGJtlsF8lwXkFKlUPIXYdlkvXj8tPbBiXjKQw2lcwlplLLWOwNjnLZJYSulviUFT8GcaGKzGQUGiCXJA2KXPA39LJInkiFFNshRz2P6n0ezL4/FV4/ATffMx1EYs3dmS+jIcCwUnjQ= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1674551734; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=BnbNJ4rl83QaRm98ZKsqY+fdltToGvVWCZDfjDbvtk0=; b=JgJROedyAkVhdA9zMMLfrhWWUhz5BI+eQdXZRDtNbOx+EKYwMdhuMm7auhKKfqGbERIkunbTmk3b8veNbhiFVDj6AZTaBUVdlDCeDmaGYweOklWA5uNDOn1KK7CWSbQeQBTQQLLPXK/bX0Ji2Hp7OUf0uXQKJFqUNsCqrzigrb0= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1674551734; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=BnbNJ4rl83QaRm98ZKsqY+fdltToGvVWCZDfjDbvtk0=; b=LlHX4m6QJLjdOLmuh05+A7GYxFrnXUFRJlPuMu/4lJm6vVhFwdSPkkjCuEKEksNU 9PsCno3ENWuKnvx8atGx1XJZqyRruKIP06EQM4l4wS0vOyr76JnC0PbpE9rPLR56TLm vd+7R7fhTeyz4l1BvgkaNATDg/uUzDY86/brblqw= Received: from localhost (196-108-142-46.pool.kielnet.net [46.142.108.196]) by mx.zohomail.com with SMTPS id 167455173251741.511579206814645; Tue, 24 Jan 2023 01:15:32 -0800 (PST) References: <20230122004951.119277-1-madalinionel.patrascu@HIDDEN> <20230122004951.119277-4-madalinionel.patrascu@HIDDEN> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus <rekado@HIDDEN> To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= <madalinionel.patrascu@HIDDEN> Subject: Re: [bug#60997] [PATCH 4/4] gnu: Add python-metaphlan. Date: Tue, 24 Jan 2023 10:11:36 +0100 In-reply-to: <20230122004951.119277-4-madalinionel.patrascu@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87cz74e1ji.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 60997 Cc: 60997 <at> debbugs.gnu.org, debbugs-submit <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu <madalinionel.patrascu@HIDDEN>= writes: > * gnu/packages/bioinformatics.scm (python-metaphlan): New variable. Unfortunately, this one is also incomplete. The package includes R code that needs to have its dependencies satisfied. It also calls out to bowtie2, and needs raxml, muscle, blast, etc. The clash of biopython versions will also need to be addressed. I=E2=80=99ll push as much as is feasible, but I=E2=80=99d like to ask you t= o rework this package definition in particular. Thanks! --=20 Ricardo
guix-patches@HIDDEN
:bug#60997
; Package guix-patches
.
Full text available.Received: (at 60997) by debbugs.gnu.org; 24 Jan 2023 09:11:38 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Jan 24 04:11:38 2023 Received: from localhost ([127.0.0.1]:55850 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1pKFL8-0003uG-Cd for submit <at> debbugs.gnu.org; Tue, 24 Jan 2023 04:11:38 -0500 Received: from sender3-of-o59.zoho.com ([136.143.184.59]:21906) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1pKFL5-0003u1-VK; Tue, 24 Jan 2023 04:11:36 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1674551493; cv=none; d=zohomail.com; s=zohoarc; b=A4PyS/ae9cUMPeVxRQzyd+ztefLctvWGfhU4CYTLL8d7NQsnMIa+C4SlBh7narUe/KmzUFyDiLDZLhQ40gPEggFE3rIc0JQo34f3PYLxG32J1F8JW8KjlOYGi6OZkjpfXBzdhy3o+JbuUxMWAPM/yrZxfXETnTyqfQ8hZXj+odY= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1674551493; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=TDUcQcE6mVm159kFQotX5iuzSWta6bqfHNVrkElKDug=; b=mxLqVOVod+ZviHCs4z087BbCSWG/6FST8DM2Ci06FV2sWIrh5hlZdihlbV7wEwHG6X6bdg5hyGaiYo4LKln6o4udborRLM/uLFzeVm4Bh1sXy74Yg55pmKL2D09yn7tdFCSJDTHeEXC/RZDikWue3JjwaIfZOfMPeju6M4K71IE= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1674551493; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=TDUcQcE6mVm159kFQotX5iuzSWta6bqfHNVrkElKDug=; b=QcJVY6tsCCEL6PVVAF83iPfeSrjfgDxqenYOfAleNZzcl0cU65cEluoT2XxeeRNm VNo2KuEHI6PUtZqp15n7lxgeU+jwLE3MLJ+N8oNP77R6rXl80M6bbGtyj3RUyVsB1mA z0F2s1DPM4MvrszbCn/qQS1+brP4qgu/0tc2rFic= Received: from localhost (196-108-142-46.pool.kielnet.net [46.142.108.196]) by mx.zohomail.com with SMTPS id 1674551491082793.5731211523502; Tue, 24 Jan 2023 01:11:31 -0800 (PST) References: <20230122004951.119277-1-madalinionel.patrascu@HIDDEN> <20230122004951.119277-3-madalinionel.patrascu@HIDDEN> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus <rekado@HIDDEN> To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= <madalinionel.patrascu@HIDDEN> Subject: Re: [bug#60997] [PATCH 3/4] gnu: Add python-phylophlan. Date: Tue, 24 Jan 2023 10:10:20 +0100 In-reply-to: <20230122004951.119277-3-madalinionel.patrascu@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87h6wge1q7.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60997 Cc: 60997 <at> debbugs.gnu.org, debbugs-submit <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu <madalinionel.patrascu@HIDDEN>= writes: > + (build-system python-build-system) Please use pyproject-build-system where possible. > + (arguments > + (list > + #:tests? #f ;pypi no tests There are no tests, nothing to do with pypi. > + #: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"))))))) I changed this to just fetch the source from git. > + (propagated-inputs > + (list python-biopython This will become a problem down the line when combined with cmseq. --=20 Ricardo
guix-patches@HIDDEN
:bug#60997
; Package guix-patches
.
Full text available.Received: (at 60997) by debbugs.gnu.org; 24 Jan 2023 08:40:17 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Jan 24 03:40:17 2023 Received: from localhost ([127.0.0.1]:55788 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1pKEqn-00034D-80 for submit <at> debbugs.gnu.org; Tue, 24 Jan 2023 03:40:17 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21050) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1pKEqk-000340-Rw for 60997 <at> debbugs.gnu.org; Tue, 24 Jan 2023 03:40:15 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1674549612; cv=none; d=zohomail.com; s=zohoarc; b=bc6TD71GAEcfnCNGqMykqWdO1+7yIIH1ndhyApVOmrsIJiXc4KF8b6HEy2aOaE9svXo38d7h5HIVS96WUD5TWs80gYzCWE2MFFbGbNS+/FaiEog7DUw5wozZE0AaYni693dqyU/qI334RrTFChSGwlDuP+/FTCHHND3jUUyiYRA= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1674549612; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=1NvaGI75mFLE0J+samKInDlERLDHCgSKldU3gsu07gE=; b=lO2c2YJQRPLlGZn4+YQOrlV5PO6AKXUu3hILizsQlIOUcaj7L4an2kKgnaknwZlB/bsG6hXi9AdQWqIcaJkdXYFzEU9hQGOZxT7HAAqU4wblznhqCxWo+OGrhZImlxySxhvMYJ4w9TchRV8BGSgWAtBPbvphJPrEMsyKRhtkbhg= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1674549612; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=1NvaGI75mFLE0J+samKInDlERLDHCgSKldU3gsu07gE=; b=HTs3GpOjlsA8YfAygfZGKNo6dBBb/QneM9E/uc4YjrvR0lNdiJ3k9lH+y5qJrGPd j7I0kTjl1EN6RyHVNLcfvDHbnuve5llI1MU4sZpq2TN3ObG/AGOB0n6hbHGNDBNx8xb op98yj3QA+ru9L3EkG54t7wp1j1ZHLA0WrJMuN9A= Received: from localhost (196-108-142-46.pool.kielnet.net [46.142.108.196]) by mx.zohomail.com with SMTPS id 1674549609714709.7792625677146; Tue, 24 Jan 2023 00:40:09 -0800 (PST) References: <55c300694f6c49f6a89a8018a3f86729@HIDDEN> <20230122004951.119277-1-madalinionel.patrascu@HIDDEN> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus <rekado@HIDDEN> To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= <madalinionel.patrascu@HIDDEN> Subject: Re: [bug#60997] [PATCH 1/4] gnu: Add python-cmseq. Date: Tue, 24 Jan 2023 09:36:39 +0100 In-reply-to: <20230122004951.119277-1-madalinionel.patrascu@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87lelse36h.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 60997 Cc: 60997 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Hi M=C4=83d=C4=83lin, > * gnu/packages/bioinformatics.scm (python-cmseq): New variable. Thanks for the patch. Unfortunately, this is incomplete: - The tool calls out to samtools (see cmseq/cmseq.py), so it needs samtools as an input and the call needs to be patched. - The README says that biopython <=3D 1.76 is needed for polymut.py. You=E2=80=99re using 1.80. > + (build-system python-build-system) Please consider using the pyproject-build-system. > + (arguments > + (list #:tests? #f )) ;pypi no tests Apparantly, there are no tests anywhere. It=E2=80=99s not a pypi problem. Please update the comment and remove that extra space after #f. > + (home-page "http://github.com/SegataLab/cmseq/") Please use HTTPS. =E2=80=9Cguix lint=E2=80=9D informs you about the redire= ct. --=20 Ricardo
guix-patches@HIDDEN
:bug#60997
; Package guix-patches
.
Full text available.Received: (at 60997) by debbugs.gnu.org; 22 Jan 2023 00:50:26 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sat Jan 21 19:50:26 2023 Received: from localhost ([127.0.0.1]:50102 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1pJOZ0-0000i3-6d for submit <at> 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 <MadalinIonel.Patrascu@HIDDEN>) id 1pJOYq-0000h4-GN for 60997 <at> 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 <at> 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?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= <madalinionel.patrascu@HIDDEN> To: <60997 <at> debbugs.gnu.org> Subject: [PATCH 3/4] gnu: Add python-phylophlan. Date: Sun, 22 Jan 2023 01:49:50 +0100 Message-ID: <20230122004951.119277-3-madalinionel.patrascu@HIDDEN> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230122004951.119277-1-madalinionel.patrascu@HIDDEN> References: <20230122004951.119277-1-madalinionel.patrascu@HIDDEN> MIME-Version: 1.0 X-Debbugs-Cc: rekado@HIDDEN Content-Transfer-Encoding: 8bit Content-Type: text/plain 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-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 60997 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -3.3 (---) * 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") -- 2.39.1
rekado@HIDDEN, guix-patches@HIDDEN
:bug#60997
; Package guix-patches
.
Full text available.Received: (at 60997) by debbugs.gnu.org; 22 Jan 2023 00:50:18 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sat Jan 21 19:50:18 2023 Received: from localhost ([127.0.0.1]:50100 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1pJOYr-0000hi-KW for submit <at> 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 <MadalinIonel.Patrascu@HIDDEN>) id 1pJOYp-0000h0-9i for 60997 <at> 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 <at> 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?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= <madalinionel.patrascu@HIDDEN> To: <60997 <at> debbugs.gnu.org> Subject: [PATCH 1/4] gnu: Add python-cmseq. Date: Sun, 22 Jan 2023 01:49:48 +0100 Message-ID: <20230122004951.119277-1-madalinionel.patrascu@HIDDEN> X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 X-Debbugs-Cc: rekado@HIDDEN Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit 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-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 60997 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -3.3 (---) * gnu/packages/bioinformatics.scm (python-cmseq): New variable. --- gnu/packages/bioinformatics.scm | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) 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 <arunisaac@HIDDEN> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@HIDDEN> ;;; Copyright © 2018 Gábor Boskovits <boskovits@HIDDEN> -;;; Copyright © 2018, 2019, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@HIDDEN> +;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@HIDDEN> ;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@HIDDEN> ;;; Copyright © 2019 Brian Leung <bkleung89@HIDDEN> ;;; Copyright © 2019 Brett Gilio <brettg@HIDDEN> @@ -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") base-commit: f088763356e88c4911ee933fdafcad6ed66a7aa3 -- 2.39.1
rekado@HIDDEN, guix-patches@HIDDEN
:bug#60997
; Package guix-patches
.
Full text available.Received: (at 60997) by debbugs.gnu.org; 22 Jan 2023 00:50:17 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sat Jan 21 19:50:17 2023 Received: from localhost ([127.0.0.1]:50098 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1pJOYr-0000hV-4F for submit <at> 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 <MadalinIonel.Patrascu@HIDDEN>) id 1pJOYo-0000gx-Kc for 60997 <at> 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 <at> 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?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= <madalinionel.patrascu@HIDDEN> To: <60997 <at> debbugs.gnu.org> Subject: [PATCH 4/4] gnu: Add python-metaphlan. Date: Sun, 22 Jan 2023 01:49:51 +0100 Message-ID: <20230122004951.119277-4-madalinionel.patrascu@HIDDEN> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230122004951.119277-1-madalinionel.patrascu@HIDDEN> References: <20230122004951.119277-1-madalinionel.patrascu@HIDDEN> MIME-Version: 1.0 X-Debbugs-Cc: rekado@HIDDEN Content-Transfer-Encoding: 8bit Content-Type: text/plain 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-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 60997 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -3.3 (---) * 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") -- 2.39.1
rekado@HIDDEN, guix-patches@HIDDEN
:bug#60997
; Package guix-patches
.
Full text available.Received: (at 60997) by debbugs.gnu.org; 22 Jan 2023 00:50:17 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sat Jan 21 19:50:17 2023 Received: from localhost ([127.0.0.1]:50096 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1pJOYq-0000hT-LU for submit <at> 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 <MadalinIonel.Patrascu@HIDDEN>) id 1pJOYo-0000gz-Kg for 60997 <at> 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 <at> 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?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= <madalinionel.patrascu@HIDDEN> To: <60997 <at> debbugs.gnu.org> Subject: [PATCH 2/4] gnu: Add python-hclust2. Date: Sun, 22 Jan 2023 01:49:49 +0100 Message-ID: <20230122004951.119277-2-madalinionel.patrascu@HIDDEN> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230122004951.119277-1-madalinionel.patrascu@HIDDEN> References: <20230122004951.119277-1-madalinionel.patrascu@HIDDEN> MIME-Version: 1.0 X-Debbugs-Cc: rekado@HIDDEN Content-Transfer-Encoding: 8bit Content-Type: text/plain 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-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 60997 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -3.3 (---) * 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") -- 2.39.1
rekado@HIDDEN, guix-patches@HIDDEN
:bug#60997
; Package guix-patches
.
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Thread-Topic: [patch] gnu: Add python-cmseq, python-cmseq, python-phylophlan and python-metaphlan. 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"MadalinIonel.Patrascu@HIDDEN" <MadalinIonel.Patrascu@HIDDEN>
:guix-patches@HIDDEN
.
Full text available.guix-patches@HIDDEN
:bug#60997
; Package guix-patches
.
Full text available.
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