From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:49396) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1g4QzB-0000Em-Bh for guix-patches@gnu.org; Mon, 24 Sep 2018 09:33:16 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1g4Qz2-0000Cj-De for guix-patches@gnu.org; Mon, 24 Sep 2018 09:33:10 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:47230) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1g4Qz0-0000C5-2x for guix-patches@gnu.org; Mon, 24 Sep 2018 09:33:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1g4Qyz-0005LL-TJ for guix-patches@gnu.org; Mon, 24 Sep 2018 09:33:01 -0400 Subject: [bug#32819] [PATCH] gnu: Add porechop. Resent-Message-ID: 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) 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) From: pimi Date: Mon, 24 Sep 2018 15:31:14 +0200 Message-ID: <20180924133114.14714-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 32819@debbugs.gnu.org Cc: ricardo.wurmus@mdc-berlin.de, pimi * 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