From debbugs-submit-bounces@debbugs.gnu.org Sat Jan 21 19:50:17 2023 Received: (at 60997) by debbugs.gnu.org; 22 Jan 2023 00:50:17 +0000 Received: from localhost ([127.0.0.1]:50098 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pJOYr-0000hV-4F for submit@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 ) id 1pJOYo-0000gx-Kc for 60997@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@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?= To: <60997@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@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de> References: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net 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@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" 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