From patchwork Sat May 18 17:26:35 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Pierre Neidhardt X-Patchwork-Id: 13998 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id A244117027; Sat, 18 May 2019 18:27:08 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 43F5317025 for ; Sat, 18 May 2019 18:27:08 +0100 (BST) Received: from localhost ([127.0.0.1]:36684 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36x-0004H0-Ri for patchwork@mira.cbaines.net; Sat, 18 May 2019 13:27:07 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48555) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36u-0004Dw-MH for guix-patches@gnu.org; Sat, 18 May 2019 13:27:05 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36t-0001LP-Bm for guix-patches@gnu.org; Sat, 18 May 2019 13:27:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47620) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hS36s-0001Kr-QE for guix-patches@gnu.org; Sat, 18 May 2019 13:27:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hS36s-0007u9-La for guix-patches@gnu.org; Sat, 18 May 2019 13:27:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#35792] [PATCH 2/7] gnu: Add smithwaterman. Resent-From: Pierre Neidhardt Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 18 May 2019 17:27:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 35792 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 35792@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.155820041430305 (code B ref -1); Sat, 18 May 2019 17:27:02 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:54 +0000 Received: from localhost ([127.0.0.1]:32916 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sc-1s for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:54 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34077) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36h-0007s7-I6 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:51 -0400 Received: from lists.gnu.org ([209.51.188.17]:32860) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36a-00018Y-H4 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:44 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48418) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36Z-0004D4-8u for guix-patches@gnu.org; Sat, 18 May 2019 13:26:44 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Y-00016G-7N for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:41027) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Y-000157-10 for guix-patches@gnu.org; Sat, 18 May 2019 13:26:42 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id 04FEC240011 for ; Sat, 18 May 2019 17:26:40 +0000 (UTC) From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:35 +0200 Message-Id: <20190518172640.7165-2-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 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-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 * gnu/packages/bioinformatics.scm (smithwaterman): 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 244741854d..1bf33853b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14869,3 +14869,33 @@ might be caused by ATAC-seq library prep or sequencing. The main program, (description "This is a C++ wrapper around the Tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) + +(define-public smithwaterman + ;; TODO: Upgrading smithwaterman breaks FreeBayes. + (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) + (package + (name "smithwaterman") + (version (string-append "0-1." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/smithwaterman/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "smithwaterman" bin))))))) + (home-page "https://github.com/ekg/smithwaterman") + (synopsis "Implementation of the Smith-Waterman algorithm") + (description "Implementation of the Smith-Waterman algorithm.") + ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. + (license (list license:gpl2 license:expat)))))