From unknown Mon Jun 23 16:45:02 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#32819 <32819@debbugs.gnu.org> To: bug#32819 <32819@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add porechop. Reply-To: bug#32819 <32819@debbugs.gnu.org> Date: Mon, 23 Jun 2025 23:45:02 +0000 retitle 32819 [PATCH] gnu: Add porechop. reassign 32819 guix-patches submitter 32819 pimi severity 32819 normal tag 32819 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 24 09:32:14 2018 Received: (at submit) by debbugs.gnu.org; 24 Sep 2018 13:32:14 +0000 Received: from localhost ([127.0.0.1]:51488 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g4QyD-0005KI-Nr for submit@debbugs.gnu.org; Mon, 24 Sep 2018 09:32:13 -0400 Received: from eggs.gnu.org ([208.118.235.92]:39498) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g4QyB-0005K2-Jn for submit@debbugs.gnu.org; Mon, 24 Sep 2018 09:32:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1g4Qy3-0008IK-Gt for submit@debbugs.gnu.org; Mon, 24 Sep 2018 09:32:06 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.0 required=5.0 tests=BAYES_40,T_DKIM_INVALID autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:49892) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1g4Qxx-0008Gd-TS for submit@debbugs.gnu.org; Mon, 24 Sep 2018 09:32:00 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:49090) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1g4Qxq-0007YC-JG for guix-patches@gnu.org; Mon, 24 Sep 2018 09:31:57 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1g4Qxn-0008CT-UY for guix-patches@gnu.org; Mon, 24 Sep 2018 09:31:50 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:58058) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1g4Qxn-00087H-FH for guix-patches@gnu.org; Mon, 24 Sep 2018 09:31:47 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 720A71356D9A for ; Mon, 24 Sep 2018 15:31:44 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:x-mailer:message-id:date :date:subject:subject:from:from:received:received:received; s= mdc; t=1537795899; x=1539610300; bh=jGRaTGK/sK9PsxXHlOeSasOQf0Ds mrdjmoqcKnJCTTs=; b=IfLl/Wz8LAf6PQuab5VqVP6N7O40IP59s+22XZLb/+7J wPrAIxDN0Y2QdmaHFP7l3fO4t9FEjIzZi2uKCF0094z6Zk1C9MuWWuat/1VXz9EA U0lwfxXlRH1k2Hrne9h1WKC/JTr5Q9dxBW2cf0DPkAyvk7ggDFH7gtZNY3H9UxQ= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id ZdHV0q-ZZxIJ for ; Mon, 24 Sep 2018 15:31:39 +0200 (CEST) Received: from SW-IT-P-CAS2.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Mon, 24 Sep 2018 15:31:39 +0200 (CEST) Received: from biadmin-KVM.nat (141.80.113.106) by SW-IT-P-CAS2.mdc-berlin.net (141.80.113.54) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 24 Sep 2018 15:31:28 +0200 From: pimi To: Subject: [PATCH] gnu: Add porechop. Date: Mon, 24 Sep 2018 15:31:14 +0200 Message-ID: <20180924133114.14714-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24116.000 X-TM-AS-Result: No-4.948900-8.000000-10 X-TMASE-MatchedRID: riRbj5ZX+8p7qToVEfwBPAPZZctd3P4Bo0vKTsE6kOcR34ro7k23nQDE vnsMB9SgUtir88BGn9mlfFENwMmekqjfUgfCdm6hu72KpAktHS+usS9CiBzL8SgVbxW7FDOVHsc pUFouOmsvY0FORnTTFS71R/jxbyBoViFDIhhiYLixo9yzdPhMvX0tCKdnhB58hYfw868k05Yzqx 6DtfVZtvcUt5lc1lLgKIzdZS3ou0V/KJ5+FqqOI9CC9jN7wfiyWlP6bJ4X772txN3MbcXyVZFaS fJ3q2a9qWbEY1i05zGvAmPqOTvM4hTduVseAL/iuH4McQwt1RQV4remnWxifeiPYvP0WKzlGj81 Ipo8t/JeZSAxBsC8ng== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.948900-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24116.000 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.3 (----) X-Debbugs-Envelope-To: submit Cc: ricardo.wurmus@mdc-berlin.de, pimi 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: -5.3 (-----) * gnu/packages/bioinformatics.scm (porechop): 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 b619866ba..2ab7135f5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13760,3 +13760,33 @@ sequencing data.") ;; This is free software but the license variant is unclear: ;; . (license license:bsd-3))) + +(define-public porechop + ;; The recommended way to install is to clone the git repository + ;; https://github.com/rrwick/Porechop#installation + (let ((commit "289d5dca4a5fc327f97b3f8cecb68ecaf1014861") + (revision "1")) + (package + (name "porechop") + (version (git-version "0.2.3" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rrwick/Porechop.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05ps43gig0d3ia9x5lj84lb00hbsl6ba9n7y7jz927npxbr2ym23")))) + (build-system python-build-system) + (home-page "https://github.com/rrwick/porechop") + (synopsis "Finding, trimming or splitting adapters, in Oxford Nanopore reads") + (description + "The porechop package is a tool for finding and removing adapters from Oxford +Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read +has an adapter in its middle, it is treated as chimeric and chopped into +separate reads. Porechop performs thorough alignments to effectively find +adapters, even at low sequence identity. Porechop also supports demultiplexing +of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR +Barcoding Kit or Rapid Barcoding Kit.") + (license license:gpl3)))) -- 2.17.1 From debbugs-submit-bounces@debbugs.gnu.org Sun Sep 30 14:11:04 2018 Received: (at 32819-done) by debbugs.gnu.org; 30 Sep 2018 18:11:04 +0000 Received: from localhost ([127.0.0.1]:60203 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g6gBL-0001L6-Pw for submit@debbugs.gnu.org; Sun, 30 Sep 2018 14:11:03 -0400 Received: from wout2-smtp.messagingengine.com ([64.147.123.25]:53269) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g6gBI-0001KW-Vg for 32819-done@debbugs.gnu.org; Sun, 30 Sep 2018 14:11:02 -0400 Received: from compute4.internal (compute4.nyi.internal [10.202.2.44]) by mailout.west.internal (Postfix) with ESMTP id BE047C15; Sun, 30 Sep 2018 14:10:59 -0400 (EDT) Received: from mailfrontend2 ([10.202.2.163]) by compute4.internal (MEProxy); Sun, 30 Sep 2018 14:11:00 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=cc:content-type:date:from:in-reply-to:message-id:mime-version :references:subject:to:x-me-sender:x-me-sender:x-sasl-enc; s= mesmtp; bh=Ws8CXdfnDAWNq5cn5o6knjUvAPanWPe5K8JrnP4Hp7c=; b=LcGHw 4bDlJhSh79yE9XwS+1eDPRjPYVXw3+D2CPhE0quoIFQmhikZZjS5e9IfWj5VMGIk 8E6fprN/9a2YW67IYQw5j2zwrXU6/IiVZ4noG8VJciR3183bpUR12RCw8kRmku0a aBxnYlYvdBuNMODBLEtKs6FEJSXhvrifRyFVtM= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:from:in-reply-to :message-id:mime-version:references:subject:to:x-me-sender :x-me-sender:x-sasl-enc; s=fm3; bh=Ws8CXdfnDAWNq5cn5o6knjUvAPanW Pe5K8JrnP4Hp7c=; b=O2H7JPDhgvwBvUeCWBl22x2Vrkwim0wmBQ/ikXUQXUFL2 QfU2BgtvwdtlzPw/aB76B0YMI2QXMyAjwa7SMpFKuUiQlFZ8m6YlQc8+Oi6zPmUb roaXTtSLRaWbrGV7C1ezPTeUk2G/oluBHBtGKVKBklGfvXlPSZaebjHr+LPs8iQu bWDSNHZyI1S8Uy7KB6bxeBkLACb1HVAP4GgnfKZd/R6/9yUzRV2rvQwerAduODps x9q8d/FV01sjnGHrMDliHeIqgr0IozibV3nFfEympIZ9mWkiRaBEFuuYrQ8CnPxN wmPHSS24qJcMKhg4Xolew5ScbOhn78MVELkDaxbIA== X-ME-Proxy: X-ME-Sender: Received: from localhost (unknown [172.58.200.226]) by mail.messagingengine.com (Postfix) with ESMTPA id 7B9EF102DE; Sun, 30 Sep 2018 14:10:58 -0400 (EDT) Date: Sun, 30 Sep 2018 14:10:57 -0400 From: Leo Famulari To: pimi Subject: Re: [bug#32819] [PATCH] gnu: Add porechop. Message-ID: <20180930181057.GA5218@jasmine.lan> References: <20180924133114.14714-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="pWyiEgJYm5f9v55/" Content-Disposition: inline In-Reply-To: <20180924133114.14714-1-madalinionel.patrascu@mdc-berlin.de> User-Agent: Mutt/1.10.1 (2018-07-13) X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 32819-done Cc: 32819-done@debbugs.gnu.org, ricardo.wurmus@mdc-berlin.de 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: -1.7 (-) --pWyiEgJYm5f9v55/ Content-Type: text/plain; charset=us-ascii Content-Disposition: inline On Mon, Sep 24, 2018 at 03:31:14PM +0200, pimi wrote: > * gnu/packages/bioinformatics.scm (porechop): New variable. Thanks! > + (license license:gpl3)))) I used gpl3+ and pushed as f2bc53af70eea7b7147b9e7e40280941866ed128 For more information about the license, see here: --pWyiEgJYm5f9v55/ Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCAAdFiEEsFFZSPHn08G5gDigJkb6MLrKfwgFAluxEbEACgkQJkb6MLrK fwgQ0RAAvU582ZkRAui0hhwQMMxvMUgZZo/Uq6H5nFQNn8A/LiJrzU5gh2n0vw9f fPYNdYc1XLVl1oHM6TOCfFRLEW4dXWNqRnXWuonKgRVrq1+OsUvWOyN2udazbAYJ x+u4LpOOpVAdEFlVciIO7yIBvKxRMbe/6ho0sgcehJ3NkiE0smY2a3Ynhgr6RXT/ xbo/G0RVE9Ij7ghaJcM1d44ZWztPFHhvMb6uQ+QUV07KSHEayY7DdGHzz/NFj+i0 1x2mXxL4LS8eKBnS50H8c6QDO7Ga+b4QIlqltP894eNRFH/GhCLQUWpEqVv3IqAC W/0heYRDv4tkUMa9fHfPW1PYfypi/+qhGh5qs0mlma2fh7fyGWZm8zhq8vD6waSZ PK7vvAPZmAsJ1GWJOzzIaZTFvag3/XBpuvQ2VifcTK4JfST9qDD2AqxgkVGbDw3/ fSIPdywDgPPHTtsh1NDVubA3YWmn2D5J4yZUNolsIsXvtqJawwsGnd/c8jEWekm0 rO70RF3bYwq62y41KMV4//MWhI5Bb2lngyLN2nLlqZYVLyaQqrZPOfGBVzLj/pyr xilCcutFF2gK4DoLRKIuZbKkEOoo2JzYCIUerKpiHPqQEbizr/1iOCCCCmJSIvQl hvJNQS0eJExh1ShaI2qaVF6H9VDgUAeeEIqYu2XxOSz1TKEikGo= =La9J -----END PGP SIGNATURE----- --pWyiEgJYm5f9v55/-- From unknown Mon Jun 23 16:45:02 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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