From patchwork Sun May 15 04:36:44 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Maxim Cournoyer X-Patchwork-Id: 39325 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 57DDD27BBEA; Sun, 15 May 2022 06:00:11 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 0575827BBE9 for ; Sun, 15 May 2022 06:00:11 +0100 (BST) Received: from localhost ([::1]:59774 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nq6MU-0003PA-36 for patchwork@mira.cbaines.net; Sun, 15 May 2022 01:00:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43444) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nq6IY-0000VF-EB for guix-patches@gnu.org; Sun, 15 May 2022 00:56:10 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54372) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nq6IX-0006ar-GF for guix-patches@gnu.org; Sun, 15 May 2022 00:56:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nq6IX-0003Zp-Fr for guix-patches@gnu.org; Sun, 15 May 2022 00:56:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55424] [PATCH 017/602] gnu: Remove ribodiff. Resent-From: Maxim Cournoyer Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 15 May 2022 04:56:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55424 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55424@debbugs.gnu.org Cc: Maxim Cournoyer Received: via spool by 55424-submit@debbugs.gnu.org id=B55424.165259052313306 (code B ref 55424); Sun, 15 May 2022 04:56:05 +0000 Received: (at 55424) by debbugs.gnu.org; 15 May 2022 04:55:23 +0000 Received: from localhost ([127.0.0.1]:48167 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nq6Hq-0003SR-Pr for submit@debbugs.gnu.org; Sun, 15 May 2022 00:55:23 -0400 Received: from mail-qk1-f170.google.com ([209.85.222.170]:47091) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nq69u-0002uE-VB for 55424@debbugs.gnu.org; Sun, 15 May 2022 00:47:11 -0400 Received: by mail-qk1-f170.google.com with SMTP id c1so10164077qkf.13 for <55424@debbugs.gnu.org>; Sat, 14 May 2022 21:47:10 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=sGP3pBMS1XUONT0hvVUjMhK9lhPspBt0WosXLFZHxV4=; b=Q3pdNrnQOXaLvg29jynLOXaqEVA+oGj3lxwEzKg1Y4JisQ5xn1lb+aiTLUQAgajTrH nXQSepts3KKM6hm1Cr1QJvMsL3gBhgErSG0mbRjcF5hfEv0lIiDZSEE2qJ7PYuFcjs0O r1pxVaF7i9aE+rK6WAqenCrKax7JKHAoAkR5gGE1sPXsr0ybojH2tpvIQXIFhro4uAxs pHewvs3RKtOUMma/cCAwy2L0CYNV512GaF8dkElgVNaEpU3gtnDL0+tjq7erwx3n4GTc 0MSYTro2i4YcimrmANCyJwvkXl9rsQ/+K2qwzuoH8+8eX16aXWXQyJXPhIocaOHB8+5m k1zg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=sGP3pBMS1XUONT0hvVUjMhK9lhPspBt0WosXLFZHxV4=; b=0he4nkitLDv70PerJwuvqABgvPtHOPWby+7AqNzR4dvPZ6aQ64987VWHf0eccD1pDk FyJZ/zBDbFMRCqn2fsxet40tPa9DxzxKv9FHSSxQ9YhOieg5wVY4SmGs1ieW8+NQGbFt Ng95UF9POC1ugN2G23K2+iAa+u01XWdzCWkaDn3mKAdgg3j1NNCDMGAD1PgqCB3XgF1w Zi6MM2HMfQeN4YhrpJtJ/v3v8B0U632by7msxt4icmTKwzj2YzWi6oY7ltJ252ReZ0aG YroxG+3wsejSetZSx2hRdHwlydVTd45J+JsBoWpCXimUAbRip6K6E1CSbdFQaeIB3NVt WtDQ== X-Gm-Message-State: AOAM530TfSqhUPPtIHM/AKyS8bLqflgO91Iq3PK8DadIvEbOFlJrZ3ym kdzLwMBe07ciugmEwZhqXS+5GbnZTrZK8Q== X-Google-Smtp-Source: ABdhPJz5dtThTPwXqUy8gpFcvTKJ1Tl7HajVSWSQqxm1g1cdaRZExfdUpR9ibtFvNhR/HRuCeYfiew== X-Received: by 2002:a05:620a:2848:b0:67d:35de:bb5b with SMTP id h8-20020a05620a284800b0067d35debb5bmr8472741qkp.499.1652590025345; Sat, 14 May 2022 21:47:05 -0700 (PDT) Received: from localhost.localdomain (dsl-149-239.b2b2c.ca. [66.158.149.239]) by smtp.gmail.com with ESMTPSA id 2-20020ac82082000000b002f39b99f672sm4287690qtd.12.2022.05.14.21.47.04 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 14 May 2022 21:47:05 -0700 (PDT) From: Maxim Cournoyer Date: Sun, 15 May 2022 00:36:44 -0400 Message-Id: <20220515044629.6843-17-maxim.cournoyer@gmail.com> X-Mailer: git-send-email 2.36.0 In-Reply-To: <20220515044629.6843-1-maxim.cournoyer@gmail.com> References: <20220515044629.6843-1-maxim.cournoyer@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list 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 (ribodiff): Delete variable. --- gnu/packages/bioinformatics.scm | 46 --------------------------------- 1 file changed, 46 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c754cdb176..902e65394d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -839,52 +839,6 @@ (define-public ribotaper provides the Ribotaper pipeline.") (license license:gpl3+))) -(define-public ribodiff - (package - (name "ribodiff") - (version "0.2.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ratschlab/RiboDiff") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - ;; This test fails because of the matplotlib plotting backend. - (add-after 'unpack 'disable-plot-test - (lambda _ - (substitute* "src/ribodiff/functional_test_te.py" - (("pl\\.make_plots\\(data, opts\\)") "#")))) - ;; Generate an installable executable script wrapper. - (add-after 'unpack 'patch-setup.py - (lambda _ - (substitute* "setup.py" - (("^(.*)packages=.*" line prefix) - (string-append line "\n" - prefix "scripts=['scripts/TE.py'],\n")))))))) - (inputs - (list python2-numpy python2-matplotlib python2-scipy - python2-statsmodels)) - (native-inputs - (list python2-mock python2-nose)) - (home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") - (synopsis "Detect translation efficiency changes from ribosome footprints") - (description "RiboDiff is a statistical tool that detects the protein -translational efficiency change from Ribo-Seq (ribosome footprinting) and -RNA-Seq data. It uses a generalized linear model to detect genes showing -difference in translational profile taking mRNA abundance into account. It -facilitates us to decipher the translational regulation that behave -independently with transcriptional regulation.") - (license license:gpl3+))) - (define-public bioawk (package (name "bioawk")