From patchwork Sat May 18 17:26:36 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Pierre Neidhardt X-Patchwork-Id: 14002 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 4C13117027; Sat, 18 May 2019 18:27:22 +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 3E7D81701E for ; Sat, 18 May 2019 18:27:21 +0100 (BST) Received: from localhost ([127.0.0.1]:36694 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS37A-0004Qj-Mi for patchwork@mira.cbaines.net; Sat, 18 May 2019 13:27:20 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48571) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36v-0004Dz-5i for guix-patches@gnu.org; Sat, 18 May 2019 13:27:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36t-0001LX-Ce for guix-patches@gnu.org; Sat, 18 May 2019 13:27:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47621) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hS36t-0001LA-9I 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 1hS36t-0007uG-3q for guix-patches@gnu.org; Sat, 18 May 2019 13:27:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#35792] [PATCH 3/7] gnu: Add multichoose. 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.155820041530319 (code B ref -1); Sat, 18 May 2019 17:27:03 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:55 +0000 Received: from localhost ([127.0.0.1]:32919 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sk-ET for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:55 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34082) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36h-0007s9-J3 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:52 -0400 Received: from lists.gnu.org ([209.51.188.17]:47058) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36b-00019L-Eq for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:46 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48434) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36Z-0004D6-Vi for guix-patches@gnu.org; Sat, 18 May 2019 13:26:45 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Y-00016i-Io for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:50409) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Y-00015P-8B 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 3633224000A for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:36 +0200 Message-Id: <20190518172640.7165-3-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 (multichoose): New variable. --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1bf33853b0..3ff0f69f5e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14899,3 +14899,39 @@ some of the details of opening and jumping in tabix-indexed files.") (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))))) + +(define-public multichoose + (package + (name "multichoose") + (version "1.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/multichoose/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs")))) + (build-system gnu-build-system) + (native-inputs + `(("python" ,python-2) + ("node" ,node))) + (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"))) + ;; TODO: There are Python modules for these programs too. + (install-file "multichoose" bin) + (install-file "multipermute" bin))))))) + (home-page "https://github.com/ekg/multichoose") + (synopsis "Efficient loopless multiset combination generation algorithm") + (description "This library implements an efficient loopless multiset +combination generation algorithm which is (approximately) described in +\"Loopless algorithms for generating permutations, combinations, and other +combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), +1973. (Algorithm 7.)") + (license license:expat)))