Ricardo Wurmus <rekado@HIDDEN>
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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.
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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
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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.
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* 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.
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Subject: [PATCH 1/4] gnu: Add python-cmseq.
Date: Sun, 22 Jan 2023 01:49:48 +0100
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* 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.
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Subject: [PATCH 4/4] gnu: Add python-metaphlan.
Date: Sun, 22 Jan 2023 01:49:51 +0100
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* 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.
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Subject: [PATCH 2/4] gnu: Add python-hclust2.
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* 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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From: "MadalinIonel.Patrascu@HIDDEN"
<MadalinIonel.Patrascu@HIDDEN>
To: "guix-patches@HIDDEN" <guix-patches@HIDDEN>
Subject: [patch] gnu: Add python-cmseq, python-cmseq, python-phylophlan and
python-metaphlan.
Thread-Topic: [patch] gnu: Add python-cmseq, python-cmseq, python-phylophlan
and python-metaphlan.
Thread-Index: AQHZLfqNKAajzniyX0qyS9ynh86QIQ==
Date: Sun, 22 Jan 2023 00:44:01 +0000
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