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Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 16 Dec 2019 15:27:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 38637 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <38637@debbugs.gnu.org> Cc: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Received: via spool by 38637-submit@debbugs.gnu.org id=B38637.15765099812468 (code B ref 38637); Mon, 16 Dec 2019 15:27:03 +0000 Received: (at 38637) by debbugs.gnu.org; 16 Dec 2019 15:26:21 +0000 Received: from localhost ([127.0.0.1]:40236 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsGK-0000dk-Vm for submit@debbugs.gnu.org; Mon, 16 Dec 2019 10:26:21 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:53387) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsGI-0000db-Sk for 38637@debbugs.gnu.org; Mon, 16 Dec 2019 10:26:19 -0500 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 609A6160087 for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:18 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1576509977; x=1578324378; bh=WdL9SvRpcJJrzI72S/HlsQA2MPbNLi8d3H5jyPRkuOM=; b=FAg2vCvQD56D hL0MhAbXeAo1aBtRgJxJn/yOJXdYCTox3Nj14viyWnzgzcWnBWclH1sTHDi6m5mo uPsLtY/0MYhMh2XIs81kl57PxsFYJmcHWn/kxRA/onVih9uzHQweHRYo40WXbBjU oPFl23AR7Fv+RA0+vh5313pnXg4d/M8= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 4_CPqCxcpZjV for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:17 +0100 (CET) Received: from SW-IT-P-CAS4.mdc-berlin.net (mgw10-4.mdc-berlin.de [141.80.113.59]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:17 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.468.0; Mon, 16 Dec 2019 16:26:17 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 16 Dec 2019 16:25:19 +0100 Message-ID: <20191216152519.3595-4-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 In-Reply-To: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> References: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-AS-Result: No-9.684700-8.000000-10 X-TMASE-MatchedRID: cDFwyY+CAdryD+EqUBix4ZzEHTUOuMX3S1zwNuiBtITdacCPv0XN4gSm rW+u3NBf8Tx6bfhlbmfqc3eDqWRWoMVVIEyvZyb0N8QmGQ8nUhrIEQTlh1/QMatkcxxU6EVIeyY Rtv+ZW85LVtcjSeah83NERYbQXfHtb52irmhQ5bIHwXE78FAewgRryDXHx6oXOK4yXNWF4bBfPe q3iAoZIjZMBH4YYyYkhbopPwYOhRPnxyk6kt+DQ8sK9y5C/Fiy4k1wcu9E2kRO5bh7WmoyDRaQe ocCrFbE5R08LIISReJChbrzKpI3S3XZkAUtUetntgyUiC29Qd7rixWWWJYrHx8TzIzimOwP8dA3 q/uj/L/EQdG7H66TyF82MXkEdQ77ZpGYo2OTDe+K4HLwdlBk9sFvLeqZLHq5YPD+d6Fcm0TeBYH HPMO4Xw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--9.684700-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-SNTS-SMTP: 1505AEE8AEB2799CBB2C1D5A395228D630B5CCEA83E07A220BFF2974FE49163E2000:9 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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" X-getmail-retrieved-from-mailbox: Patches Co-authored-by: Ricardo Wurmus * gnu/packages/bioinformatics.scm (python-gffutils): New variable. --- gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c8396a33dd..14c0b59067 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15370,3 +15370,54 @@ methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.") ;; See https://github.com/dpryan79/MethylDackel/issues/85 (license license:expat))) + +(define-public python-gffutils + ;; The latest release is older more than a year than the latest commit + (let ((commit "4034c54600813b1402945e12faa91b3a53162cf1") + (revision "1")) + (package + (name "python-gffutils") + (version (git-version "0.9" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/daler/gffutils.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rwafjdnbir5wnk0ap06ww4lra3p5frhy7mfs03rlldgfnwxymsn")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + ;; Tests need to access the HOME directory + (setenv "HOME" "/tmp") + (invoke "nosetests" "-a" "!slow"))) + (add-after 'unpack 'make-gz-files-writable + (lambda _ + (for-each make-file-writable + (find-files "." "\\.gz")) + #t))))) + (propagated-inputs + `(("python-argcomplete" ,python-argcomplete) + ("python-argh" ,python-argh) + ("python-biopython" ,python-biopython) + ("python-pybedtools" ,python-pybedtools) + ("python-pyfaidx" ,python-pyfaidx) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six))) + (native-inputs + `(("python-nose" , python-nose))) + (home-page "https://github.com/daler/gffutils") + (synopsis "Tool for manipulation of GFF and GTF files") + (description + "python-gffutils is a Python package for working with and manipulating the +GFF and GTF format files typically used for genomic annotations. The files are +loaded into a sqlite3 database, allowing much more complex manipulation of +hierarchical features (e.g., genes, transcripts, and exons) than is possible +with plain-text methods alone.") + (license license:expat)))) ;; MIT license