From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 78597138334 for ; Tue, 16 Oct 2018 17:47:37 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 44CF0E088D; Tue, 16 Oct 2018 17:47:36 +0000 (UTC) Received: from smtp.gentoo.org (dev.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 14C96E088D for ; Tue, 16 Oct 2018 17:47:35 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id E93AD335C7F for ; Tue, 16 Oct 2018 17:47:32 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 17DBB391 for ; Tue, 16 Oct 2018 17:47:31 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1539712028.f7eaea4317cca5c6ca5566c05c69b604d7312bc8.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/SPAdes/SPAdes-3.12.0.ebuild sci-biology/SPAdes/SPAdes-3.13.0.ebuild X-VCS-Directories: sci-biology/SPAdes/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: f7eaea4317cca5c6ca5566c05c69b604d7312bc8 X-VCS-Branch: master Date: Tue, 16 Oct 2018 17:47:31 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: a899c3e3-6a47-452c-9111-bb974be4955d X-Archives-Hash: a1c2a103930d01e09c1e0f3f33fc2d5f commit: f7eaea4317cca5c6ca5566c05c69b604d7312bc8 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Tue Oct 16 17:47:08 2018 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Oct 16 17:47:08 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7eaea43 sci-biology/SPAdes: version bump, drop old and buggy version SPAdes 3.13.0 CHANGE: Switched to multi-k-mer mode in rnaSPAdes, k-mer values are detected automatically based on read length. CHANGE: Added manual as README.md in markdown format for github. FIX: Updated BWA and switched to RopeBWT, which allows to handle large graphs. FIX: Assert for path.length() > 0 in rnaSPAdes. FIX: CQF and k-mer counting. REMOVE: dipSPAdes module. Package-Manager: Portage-2.3.51, Repoman-2.3.10 sci-biology/SPAdes/{SPAdes-3.12.0.ebuild => SPAdes-3.13.0.ebuild} | 1 - 1 file changed, 1 deletion(-) diff --git a/sci-biology/SPAdes/SPAdes-3.12.0.ebuild b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild similarity index 96% rename from sci-biology/SPAdes/SPAdes-3.12.0.ebuild rename to sci-biology/SPAdes/SPAdes-3.13.0.ebuild index b56180a1a..00ccc4f27 100644 --- a/sci-biology/SPAdes/SPAdes-3.12.0.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild @@ -12,7 +12,6 @@ HOMEPAGE="http://cab.spbu.ru/software/spades" SRC_URI=" https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz http://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html - http://cab.spbu.ru/files/release${PV}/manual.md -> ${P}_manual.md http://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html http://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html http://spades.bioinf.spbau.ru/release3.11.1/dipspades_manual.html -> ${P}_dipspades_manual.html"