From patchwork Sun Sep 25 21:17:28 2016 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Marius Bakke X-Patchwork-Id: 15997 Received: (qmail 10188 invoked by uid 89); 25 Sep 2016 21:18:43 -0000 Authentication-Results: sourceware.org; auth=none X-Virus-Checked: by ClamAV 0.99.2 on sourceware.org X-Virus-Found: No X-Spam-SWARE-Status: No, score=-4.9 required=5.0 tests=AWL, BAYES_00, FREEMAIL_FROM, RP_MATCHES_RCVD, SPF_PASS autolearn=ham version=3.3.2 spammy=CLI, contract X-Spam-Status: No, score=-4.9 required=5.0 tests=AWL, BAYES_00, FREEMAIL_FROM, RP_MATCHES_RCVD, SPF_PASS autolearn=ham version=3.3.2 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on sourceware.org X-Spam-Level: X-HELO: lists.gnu.org Received: from lists.gnu.org (HELO lists.gnu.org) (208.118.235.17) by sourceware.org (qpsmtpd/0.93/v0.84-503-g423c35a) with ESMTP; Sun, 25 Sep 2016 21:18:32 +0000 Received: from localhost ([::1]:40449 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1boGog-0002OB-Tw for patchwork@sourceware.org; Sun, 25 Sep 2016 17:18:30 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:45322) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1boGoT-0002Jr-BA for guix-devel@gnu.org; Sun, 25 Sep 2016 17:18:18 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1boGoQ-0004bD-V6 for guix-devel@gnu.org; Sun, 25 Sep 2016 17:18:16 -0400 Received: from out2-smtp.messagingengine.com ([66.111.4.26]:59671) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1boGoO-0004Yt-Mp for guix-devel@gnu.org; Sun, 25 Sep 2016 17:18:14 -0400 Received: from compute4.internal (compute4.nyi.internal [10.202.2.44]) by mailout.nyi.internal (Postfix) with ESMTP id E5A44204B0; Sun, 25 Sep 2016 17:18:03 -0400 (EDT) Received: from frontend1 ([10.202.2.160]) by compute4.internal (MEProxy); Sun, 25 Sep 2016 17:18:03 -0400 DKIM-Signature: v=1; a=rsa-sha1; c=relaxed/relaxed; d=fastmail.com; h=cc :date:from:in-reply-to:message-id:references:subject:to :x-sasl-enc:x-sasl-enc; s=mesmtp; bh=qovl66vnX5Gou83EE/f+Pikf7v4 =; b=DF6iHIXW+2T+25bayNcejBHamoRwGzHGRwzDBZFtjIyQ1t3ul9go+vdc2iZ iuuLsz+cvG+GhMigDWwJ9iaR1RCnbnm0vC/r7tMLD5iaGsaFcmru3gBRMG36eLEH rnLuEYThYWdsIf1Ng8+7t0KhoTmOnPFlS1x8rONcBb1Ov14M= DKIM-Signature: v=1; a=rsa-sha1; c=relaxed/relaxed; d= messagingengine.com; h=cc:date:from:in-reply-to:message-id :references:subject:to:x-sasl-enc:x-sasl-enc; s=smtpout; bh=qovl 66vnX5Gou83EE/f+Pikf7v4=; b=mdH878ZyJ0B5PQH9NgAQKBm9gsYGJKjIdrk+ yGc2D7fMDZDMkQRAIgxByQtwngbAXX3gUZ9fvxJEc9t6WjU3ox1zNmNtUjGhs3H5 V1YTh6pdvj0h/cFhVYIRicffEifjXvH5qdXIfc+x7wowsqPNnW8EZm43D7Y/jptu cvSjwGQ= X-Sasl-enc: 875l3AAys5LWG5pr/j6GYSryBQVgMUsPpqnGUL9+39D6 1474838283 Received: from localhost (unknown [2.124.155.177]) by mail.messagingengine.com (Postfix) with ESMTPA id 79AFAF29CC; Sun, 25 Sep 2016 17:18:03 -0400 (EDT) From: Marius Bakke To: guix-devel@gnu.org Subject: [PATCH 4/4] gnu: Add python2-pbcommand. Date: Sun, 25 Sep 2016 22:17:28 +0100 Message-Id: <20160925211728.7636-4-mbakke@fastmail.com> X-Mailer: git-send-email 2.10.0 In-Reply-To: <20160925211728.7636-1-mbakke@fastmail.com> References: <20160925211728.7636-1-mbakke@fastmail.com> X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 66.111.4.26 X-BeenThere: guix-devel@gnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Marius Bakke Errors-To: guix-devel-bounces+patchwork=sourceware.org@gnu.org Sender: "Guix-devel" * gnu/packages/bioinformatics.scm (python2-pbcommand): New variable. --- gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1bf91a9..9343cc6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3373,6 +3373,56 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") (home-page "https://github.com/wwood/OrfM") (license license:lgpl3+))) +(define-public python2-pbcommand + ;; Upstream does not tag git releases and PyPi is out of date. + ;; See https://github.com/PacificBiosciences/pbcommand/issues/116 + (let ((revision "1") + (commit "e83a3443a1cd42b4da0d210201d711ede789917f")) + (package + (name "python2-pbcommand") + (version (string-append "0.4.11-" revision "." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PacificBiosciences/pbcommand.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1kwg84f23l7ik65qy7cxa6g5nipc2y23mppigd4j3vlzam18v52h")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 ; Python-2 only. + #:configure-flags '("--single-version-externally-managed" "--root=/") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'substitute-/bin/bash + (lambda _ + ;; Fully qualify /bin/bash for running external commands. + (substitute* "pbcommand/engine/runner.py" + (("/bin/bash") (which "bash"))) + #t)) + (replace 'check + (lambda _ (zero? (system* "nosetests" "-v"))))))) + (native-inputs + `(("python-nose" ,python2-nose) + ("python-sphinx-bootstrap-theme" ,python2-sphinx-bootstrap-theme) + ("python-sphinx-argparse" ,python2-sphinx-argparse) + ("python-tox" ,python2-tox) + ("python-setuptools" ,python2-setuptools))) + (propagated-inputs + `(("python-functools32" ,python2-functools32) + ("python-jsonschema" ,python2-jsonschema) + ("python-numpy" ,python2-numpy "out") + ("python-avro" ,python2-avro) + ("python-requests" ,python2-requests) + ("python-iso8601" ,python2-iso8601))) + (home-page "https://github.com/PacificBiosciences/pbcommand") + (synopsis "PacBio common models and CLI tool contract interface") + (description "PacBio library for common utils, models, and tools +to interface with pbsmrtpipe workflow engine.") + (license license:bsd-3)))) + (define-public python2-pbcore (package (name "python2-pbcore")