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[66.158.149.239]) by smtp.gmail.com with ESMTPSA id 2-20020ac82082000000b002f39b99f672sm4287690qtd.12.2022.05.14.21.47.11 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 14 May 2022 21:47:12 -0700 (PDT) From: Maxim Cournoyer Date: Sun, 15 May 2022 00:36:54 -0400 Message-Id: <20220515044629.6843-27-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=1652591226; 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=7LnPtVY+g/9lpHRK5GWlwRFE5USc8DQgVumaYmvEQSg=; b=l7aPDb0iStNr4ebF7KNIKr7zZ9r7JnLlJuLBRzPjZg23rxe72/lIteth94vyJHLIGukOna Iq0A/eR6KquwywiqZQ+bA7Y9Ipnwv+wZ+6U9gcm2Y9IGU9fy8wCus3c8awBS71S/Wvj0J8 TN+Eka8xyZ0kLQBSJx/Ib23mvTlnJy7cTwXtvLIVClMkfh82V0Szcbw8+TKg0hUQ6sioBn PkTjRBXCx65Qny/88GBdRCPvVh3VWrQjpINE3A1aWTshRO7kOo1poZ3i6Z16iaN2vXtuhX cngZY6cIr89ms7imGPjnDPKV/3pukZ+/dhhkRbkZbAHkev9tnL7dsWz5MxquXw== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1652591226; a=rsa-sha256; cv=none; b=ewW9ZOGw+LpJcYDnyAwIDbr7t8ZMOUbHrZyLEUnvRngglgtJv6FGaIZUshgDrn0XOcw4ia w5FEZVVzotgDIPMPGYGGzYR3s0SbtYgYp2xjN5Bx0HKfUVB8zpRVSFETsbQpco13C10rDw HawlPlKuLfZzIvgpVoLsdhLQYVpDnx4W0rnCKHiTSgjUCcSUbWdzETKYuMKQTRu/XUqAyV bsPvCjvuCQp79urdZW/8EtXfY2SDOf0zgx03/8P4qG40eCbAmtrv/pNE6o526FgvWG6KTP wiEHLB0Jn3oKGLrSYitEWaeZcwZ12j+4TjFkVac70jbfzff0EW1u8YUC0rhucQ== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=jOuuzGXg; 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: 6.17 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=jOuuzGXg; 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: 98BE63BA2A X-Spam-Score: 6.17 X-Migadu-Scanner: scn0.migadu.com X-TUID: gHpliP6fnSbd * gnu/packages/bioinformatics.scm (miso): Delete variable. --- gnu/packages/bioinformatics.scm | 48 --------------------------------- 1 file changed, 48 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b0ad03612e..d4354e8ea8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5194,54 +5194,6 @@ (define-public minced assembled metagenomic sequence.") (license license:gpl3+))) -(define-public miso - (let ((commit "b71402188000465e3430736a11ea118fd5639a4a") - (revision "1")) - (package - (name "miso") - (version (git-version "0.5.4" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/yarden/MISO/") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0x37ipwwvpxbkrg17gmq3hp92c9cphch8acd6cj7fqgnrjwd47g5")) - (modules '((guix build utils))) - (snippet - '(substitute* "setup.py" - ;; Use "gcc" instead of "cc" for compilation. - (("^defines") - "cc.set_executables( -compiler='gcc', -compiler_so='gcc', -linker_exe='gcc', -linker_so='gcc -shared'); defines"))))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 ; only Python 2 is supported - #:tests? #f)) ; no "test" target - (inputs - ;; Samtools must not be newer than 1.2. See - ;; https://github.com/yarden/MISO/issues/135 - (list samtools-1.2 python2-numpy python2-pysam python2-scipy - python2-matplotlib)) - (native-inputs - (list python2-mock ; for tests - python2-pytz)) ; for tests - (home-page "https://miso.readthedocs.io/en/fastmiso/") - (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") - (description - "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates -the expression level of alternatively spliced genes from RNA-Seq data, and -identifies differentially regulated isoforms or exons across samples. By -modeling the generative process by which reads are produced from isoforms in -RNA-Seq, the MISO model uses Bayesian inference to compute the probability -that a read originated from a particular isoform.") - (license license:gpl2)))) - (define-public muscle (package (name "muscle") -- 2.36.0