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[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 Content-Transfer-Encoding: 8bit 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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1652590820; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=sGP3pBMS1XUONT0hvVUjMhK9lhPspBt0WosXLFZHxV4=; b=mG7rYxPREfl192w69EMeJ6yHTsQIHGGN7geyPJvop89XkeL+0sQtz9MW2oeU/a5zY7tyfJ slkvxsb8zIuo1LJtyyjXkZ6uo9tGwW96BoSMGI8/A7kQdahpV/EWSvbYzJaMikfZ71Lk6/ y9IDbOGMwJUSHUQ6zObWdsnzEUlzzcmRqgJcGdRdGN75ulHWkCFi4inF48uCk9aKZDvcZb w08r+TBu4QrXn1lXjSsI5C5lVZ51/Ffnqo8kjEeSVRsZv13IjOYoGzhRPi+aY5daEIUP4c 0TO4C/0kgqT92km03KCJ6+Io0w5agKDylt+4lJuJArlbaXLZSztonMz3bPi0ow== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1652590820; a=rsa-sha256; cv=none; b=V4CZ3/XGiISC6TjNzAwlrt2oxhWNuehicp+wOSmfkBlGKwKEfnwTdbumXQlfL5C8ToDtge jEKRM/qQnkZ5JZdFzhNoXMCQVf6CHC9Nk3v5925oJRI/p0mzvWwh7lh/JbTR9KBomZxmX+ Yb1Uq6VOoMg09JHmHSpHBQssSfTzfuzUJllRFQseOvKBtXWLR2siqvTSu4sCjXl7RhzMnk JiEG87cDB859tVG0qhjVag/A87PpaCz5qImJRY+2E8xkOxttj0CAbeSSAZ0zxPJtlYKscc xEDRx110plId1/JGBnCdkH2HszCP0NomARiH8W5LtF1oYMp2BBWpuSfc3tC2ug== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=Q3pdNrnQ; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 6.47 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=Q3pdNrnQ; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 712E92B6B9 X-Spam-Score: 6.47 X-Migadu-Scanner: scn1.migadu.com X-TUID: oZ19CKLbak+4 * 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") -- 2.36.0