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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133651514707 (code B ref 53017); Tue, 04 Jan 2022 22:49:07 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:35 +0000 Received: from localhost ([127.0.0.1]:39053 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbb-0003p4-BQ for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:35 -0500 Received: from mail-wr1-f44.google.com ([209.85.221.44]:34577) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbI-0003lv-C6 for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:16 -0500 Received: by mail-wr1-f44.google.com with SMTP id s1so79182390wrg.1 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:16 -0800 (PST) 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=insOHsRBUEpQTmnQ5M+u8d8rFiGOpa9UU9H+yIAAUYM=; b=BlA6Xh2+GUoBwmM4Rql8JyjyfFoqhTnthUpYAzq4cPzhjWMJiA7HczprwQFKnu3yHJ hNPFZbIZmD+kWwOltAPqY5erzpJCTMxpYvd44YsbjJBFoPO+9nsP0RW2LyNm8tH3wy6p oYnDa3GlcrZ9XAVdyauo9SfK3aolpNaIsccOFAlU493byqIcY1kfrXZIPsdkbX3JqDNV DqIazuepH4IsCZB3DEfQ+PHYNxMGbHLB1Gge7dVZw/vPT54RiTiD6vgI1hE1gqY8x4B0 giGwffAELHRi5NDb/OBWd8K6yVq/xhmUTOo9o3TSz6DrSBwJBvMyo6jE4v+nmNJ2lvTi i/Xg== 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=insOHsRBUEpQTmnQ5M+u8d8rFiGOpa9UU9H+yIAAUYM=; b=CqcqtmlUhDPvky1tlj5KYCWb1k8wByDli69okDvPvO0QmFG3JG3aSd9Ia7VUo/k6Q2 41P+XR+yVQrJUZzfBQnyPazm26QNV15/VXh6HbTLissYAfgnEXOum1vPvqqywAYNWlG1 G28TF3BUe8EcLWRsXrH57PBvdO90Xt3GiNw+mmwSgwpnEFHizekAD4xvtb6FqusxesgZ 84pPT7vwu5sIaNTT5gJnCY2gd147uIq0YmZNktvyDqfnsNDnhNgCDthA0OE9VCdFV8eW FIT7K+smQXKekrwiYyxbrhzVmT1qmpvvHmnoJvGfDqvoA6IgfBXxLRqfHgHkKFP0Tahi agww== X-Gm-Message-State: AOAM531JAciiuaXCYhuBWu8ZY0SOKS8WOEN1HGUbn2ASBeuhn6cgpCVr tHPFT4sYHSBBAovd5z1aRR0x+ccooUU= X-Google-Smtp-Source: ABdhPJwD+J4ib8nta/X/QifdW79FHhLwCqukWF7VOEc9PAQc7+PlUx3Jnd/0seZ2hUO5xaiVTOTNPA== X-Received: by 2002:adf:d1e2:: with SMTP id g2mr45470112wrd.179.1641336490765; Tue, 04 Jan 2022 14:48:10 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.10 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:10 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:55 +0100 Message-Id: <20220104224755.1142897-17-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@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/julia-xyz.scm (julia-bioalignments): New variable. --- gnu/packages/julia-xyz.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 2e726aed23..b7a4224694 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -361,6 +361,41 @@ (define-public julia-benchmarktools benchmarks as well as comparing benchmark results.") (license license:expat))) +(define-public julia-bioalignments + (package + (name "julia-bioalignments") + (version "2.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioJulia/BioAlignments.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1wf6qgsada59r2fykxfj9hcr635wl8maqxbd3w8qpa01k9glxa0k")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'skip-test + (lambda _ + ;; Test fails because an unexpected type representation from + ;; BioSequences. The aligned value is correct though. + (substitute* "test/runtests.jl" + (("@test sprint\\(show, aln\\)") + "@test_broken sprint(show, aln)"))))))) + (propagated-inputs + (list julia-biogenerics + julia-biosequences + julia-biosymbols + julia-intervaltrees)) + (home-page "https://github.com/BioJulia/BioAlignments.jl") + (synopsis "Sequence alignement algorithm and data structures") + (description "This package provides alignement algorithms and data +structures for sequence of DNA, RNA, and amino acid sequences.") + (license license:expat))) + (define-public julia-biogenerics ;; No upstream release (let ((commit "a75abaf459250e2b5e22b4d9adf25fd36d2acab6")