From patchwork Sat May 18 17:26:38 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Pierre Neidhardt X-Patchwork-Id: 14003 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 417ED17027; Sat, 18 May 2019 18:27:32 +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 CDB4A1701E for ; Sat, 18 May 2019 18:27:31 +0100 (BST) Received: from localhost ([127.0.0.1]:36698 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS37L-0004Wi-Du for patchwork@mira.cbaines.net; Sat, 18 May 2019 13:27:31 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48597) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36w-0004GH-G0 for guix-patches@gnu.org; Sat, 18 May 2019 13:27:07 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36u-0001MT-A4 for guix-patches@gnu.org; Sat, 18 May 2019 13:27:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47623) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hS36u-0001M4-4i for guix-patches@gnu.org; Sat, 18 May 2019 13:27:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hS36u-0007uV-0w for guix-patches@gnu.org; Sat, 18 May 2019 13:27:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#35792] [PATCH 5/7] gnu: Add fastahack. Resent-From: Pierre Neidhardt Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 18 May 2019 17:27:03 +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.155820041930356 (code B ref -1); Sat, 18 May 2019 17:27:03 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:59 +0000 Received: from localhost ([127.0.0.1]:32926 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36p-0007tS-Fx for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:59 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34112) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sD-Lc for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:55 -0400 Received: from lists.gnu.org ([209.51.188.17]:49996) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36d-0001BC-QB for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:48 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48463) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36c-0004DO-G4 for guix-patches@gnu.org; Sat, 18 May 2019 13:26:47 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Z-00017K-8L for guix-patches@gnu.org; Sat, 18 May 2019 13:26:44 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:38251) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Y-00015f-KN 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 91B17240013 for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:38 +0200 Message-Id: <20190518172640.7165-5-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 (fastahack): New variable. --- gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e018b51968..3ad0a2a421 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14964,3 +14964,35 @@ combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), (description "A tiny C library for managing SOM (Self-Organizing Maps) neural networks.") (license license:gpl3)))) + +(define-public fastahack + (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd")) + (package + (name "fastahack") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/fastahack/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hfdv67l9g611i2ck4l92pd6ygmsp9g1ph4zx1ni7qkpsikf0l19")))) + (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 "fastahack" bin))))))) + (home-page "https://github.com/ekg/fastahack") + (synopsis "Indexing and sequence extraction from FASTA files") + (description "Fastahack is a small application for indexing and +extracting sequences and subsequences from FASTA files. The included library +provides a FASTA reader and indexer that can be embedded into applications +which would benefit from directly reading subsequences from FASTA files. The +library automatically handles index file generation and use.") + (license (list license:expat license:gpl2)))))