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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 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 (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")