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[66.158.149.239]) by smtp.gmail.com with ESMTPSA id 2-20020ac82082000000b002f39b99f672sm4287690qtd.12.2022.05.14.21.47.03 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 14 May 2022 21:47:04 -0700 (PDT) From: Maxim Cournoyer Date: Sun, 15 May 2022 00:36:43 -0400 Message-Id: <20220515044629.6843-16-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=1652590895; 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=RbtZLCE2VRDwRlajfQlAZtKX0nWK7OBv77vwfuy1zV8=; b=J0QXnvZWYeJIHb0zVc59YK7CQyAzjZos+bDCpYjXfTWyAEViGVEhXyuoRcuhFO592LyO/I JD8TrALaWO6Y22sFuVBXa5Q9kmgrFE4mu3ylbi+4s1KSZZEK3J+/FFUS7xZ2D1KGfeNeNo Fj/8HG6TVAOZmyeaRczAdIRzfSb5FbIzsDhJWYEc2F23TYJwvKqKrMB8qBsZZCzeXRxLaV rrG5O79aCUX7sCavsgJxZuDhdgjlCJ3rChnACh8koxsLCOWoJXMorFofuSAOxRs7S64nJW QScM1Jl03uS3yW52XiD7azxh/9+5QnTXQhvzcVlRHkjAQm/OZW7qbtff6EaOFA== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1652590895; a=rsa-sha256; cv=none; b=DXxVxfWY99lLANhrNtMEkqLmEsym4Si8gtIV406pF21P2rurb/7f6vDUWoZWt9wNv8dofD E49D8eCJiDfALl8U0jKL+vkF1gRnYKVLpTZwCGRLAax5/GcHTfmAZ1TYx10QBaW+edJyCj 4C2W6YPmfy2c1EPWcc2x0KXtgVJrmXzIg9OjU+F4nz2uqq1IM13U/3iOQZi6MSLMgiDCj1 t75jbcKeXYdfWAd17IjAQzGk1Fj/n1iADbH+aw4HQhnRH3AMhTMJLddphuy5gY+tDxfcVq V6TRC5sYTof6i9iGsy//itoUrDyxoHd8e6045cTgKKhRjU7rI25Aa08j/06FSQ== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=Yl7ZbMep; 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: 5.67 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=Yl7ZbMep; 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: 23E521B403 X-Spam-Score: 5.67 X-Migadu-Scanner: scn0.migadu.com X-TUID: eSISQEkXcLsk * gnu/packages/bioinformatics.scm (grit): Delete variable. --- gnu/packages/bioinformatics.scm | 42 --------------------------------- 1 file changed, 42 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6037a100aa..c754cdb176 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4024,48 +4024,6 @@ (define-public gemma genome-wide association studies}.") (license license:gpl3))) -(define-public grit - (package - (name "grit") - (version "2.0.5") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/nboley/grit") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'generate-from-cython-sources - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Delete these C files to force fresh generation from pyx sources. - (delete-file "grit/sparsify_support_fns.c") - (delete-file "grit/call_peaks_support_fns.c") - (substitute* "setup.py" - (("Cython.Setup") "Cython.Build")) - #t))))) - (inputs - (list python2-scipy python2-numpy python2-pysam python2-networkx)) - (native-inputs - (list python2-cython)) - ;; The canonical home page times out as of 2020-01-21. - (home-page "https://github.com/nboley/grit") - (synopsis "Tool for integrative analysis of RNA-seq type assays") - (description - "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify -full length transcript models. When none of these data sources are available, -GRIT can be run by providing a candidate set of TES or TSS sites. In -addition, GRIT can merge in reference junctions and gene boundaries. GRIT can -also be run in quantification mode, where it uses a provided GTF file and just -estimates transcript expression.") - (license license:gpl3+))) - (define-public hisat (package (name "hisat") -- 2.36.0