From debbugs-submit-bounces@debbugs.gnu.org Tue Jan 28 19:58:24 2025 Received: (at submit) by debbugs.gnu.org; 29 Jan 2025 00:58:24 +0000 Received: from localhost ([127.0.0.1]:39250 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tcwPP-0003ip-M1 for submit@debbugs.gnu.org; Tue, 28 Jan 2025 19:58:24 -0500 Received: from lists.gnu.org ([2001:470:142::17]:45688) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tcwPM-0003iX-6J for submit@debbugs.gnu.org; Tue, 28 Jan 2025 19:58:21 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tcwPG-0003HI-Ox for guix-patches@gnu.org; Tue, 28 Jan 2025 19:58:14 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tcwPC-00043A-HJ for guix-patches@gnu.org; Tue, 28 Jan 2025 19:58:14 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=systemreboot.net; s=default; t=1738112274; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding; bh=eMQs44VBo+ODpI2euepQv+Jom5uzmrBI8KfScnAxhZM=; b=XF1ZBfT/uRgvU2nGewPwT8o7G6mbLpMAFKFL3wftluXhc+tF+z/4MBnRXlovujDzRZxz3T jdLxLaPrf5XtiYGTO8+TRtppPO++OQye/2lbqA3reQI3OGgqSITdP0OVnGDzWqhgvLWpWJ ifeoguiYsosqHlH73xQ2JvxxTDg9lo/PaVXFUUs/KIB3BCfHS+2xjyiYJ0mgRBPzIulrFY 44Rc/uwgSL5J0xsRUDWd/x25mRK5qe+KfI+DC7pQvlca+4f6vNZJndCBI+EZ0pUbQ9zHuT zPf4tsnGTHkac3IePvoUYmkQXVnrekTxZB2enDXhNxq32iMcM3/VnC8OqIebSQ== Received: from localhost.localdomain ( [192.168.2.1]) by mugam.systemreboot.net (OpenSMTPD) with ESMTPSA id 1463abff (TLSv1.3:TLS_AES_256_GCM_SHA384:256:NO); Wed, 29 Jan 2025 00:57:53 +0000 (UTC) From: Arun Isaac To: guix-patches@gnu.org Subject: [PATCH] gnu: Add ravanan. Date: Wed, 29 Jan 2025 00:57:44 +0000 Message-ID: <70c9f316205a1c3c4cb88a037601e1122ca858c9.1738112213.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.47.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=139.59.75.54; envelope-from=arunisaac@systemreboot.net; helo=mugam.systemreboot.net X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.001, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.1 (/) * gnu/packages/bioinformatics.scm (ravanan): New variable. Change-Id: Ib93ea64a3a0313be167dd1cd2f036c72f1c0f138 --- gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 317c15817e8..a08f04e932a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -103,6 +103,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages golang-compression) #:use-module (gnu packages golang-xyz) #:use-module (gnu packages glib) + #:use-module (gnu packages gnupg) #:use-module (gnu packages graph) #:use-module (gnu packages graphics) #:use-module (gnu packages graphviz) @@ -134,6 +135,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages node) #:use-module (gnu packages ocaml) #:use-module (gnu packages pcre) + #:use-module (gnu packages package-management) #:use-module (gnu packages parallel) #:use-module (gnu packages pdf) #:use-module (gnu packages perl) @@ -6586,6 +6588,64 @@ (define-public cwltool CWL descriptions.") (license license:asl2.0))) +(define-public ravanan + (package + (name "ravanan") + (version "0.1.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/arunisaac/ravanan/releases/download/v" + version "/ravanan-" version ".tar.lz")) + (sha256 + (base32 + "163r3iyqfdwd3bizm36axfsvnppqwqd6zxl2vwf7sq0lcgl2zx5p")))) + (arguments + (list #:make-flags + #~(list (string-append "prefix=" #$output) + (string-append "NODE=" (search-input-file %build-inputs "bin/node"))) + #:modules `(((guix build guile-build-system) + #:select (target-guile-effective-version)) + ,@%default-gnu-imported-modules) + #:phases + (with-imported-modules `((guix build guile-build-system) + ,@%default-gnu-imported-modules) + #~(modify-phases %standard-phases + (delete 'configure) + (add-after 'install 'wrap + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (effective-version (target-guile-effective-version))) + (wrap-program (string-append out "/bin/ravanan") + `("GUILE_LOAD_PATH" prefix + (,(string-append out "/share/guile/site/" effective-version) + ,(getenv "GUILE_LOAD_PATH"))) + `("GUILE_LOAD_COMPILED_PATH" prefix + (,(string-append out "/lib/guile/" + effective-version "/site-ccache") + ,(getenv "GUILE_LOAD_COMPILED_PATH"))))))))))) + (inputs + (list bash-minimal + node + guile-3.0 + guile-filesystem + guile-gcrypt + guile-json-4 + guile-libyaml + guix)) + (native-inputs + (list lzip)) + (build-system gnu-build-system) + (home-page "https://github.com/arunisaac/ravanan") + (synopsis "High-reproducibility CWL runner powered by Guix") + (description "ravanan is a @acronym{CWL, Common Workflow Language} +implementation that is powered by GNU Guix and provides strong reproducibility +guarantees. ravanan provides strong caching of intermediate results so the +same step of a workflow is never run twice. ravanan captures logs from every +step of the workflow for easy tracing back in case of job failures. ravanan +currently runs on single machines and on slurm via its API.") + (license license:gpl3+))) + (define-public python-dendropy (package (name "python-dendropy") base-commit: e90bd12f49e08f4d30007e80eaf5649ef98b5517 -- 2.47.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 03 15:33:16 2025 Received: (at 75920) by debbugs.gnu.org; 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[86.8.111.200]) by smtp.gmail.com with ESMTPSA id ffacd0b85a97d-38c5c1cf831sm13951367f8f.90.2025.02.03.12.33.04 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 03 Feb 2025 12:33:04 -0800 (PST) From: Sharlatan Hellseher To: 75920@debbugs.gnu.org Subject: [PATCH] gnu: Add ravanan. Date: Mon, 03 Feb 2025 20:33:04 +0000 Message-ID: <87y0ymkbun.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 75920 Cc: poptsov.artyom@gmail.com X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --=-=-= Content-Type: text/plain Hi Arun, Patch visually looks ok for me. I CC Guile user to verify some other build formating otions. For some reason we have no guile team ^.- -- Oleg --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEmEeB3micIcJkGAhndtcnv/Ys0rUFAmehKAAACgkQdtcnv/Ys 0rVMBRAAmlqzcFSMIs3p1EcGSiOjFxQMPX80pjI/srgf0lv0d9zacE2B3UINei5v xDiJdQkn8MTWBqvqdjUg/WUGjuLGR67S0pKtpxzyuo4tC4zkyE3a2GmXz5SVrTjO ByS0QllnRfQ4UxLisn5NJ1B7ul6WQEEf0ic6vjZJ6umA9vndxObukkRDxiViWUQm RK0stlhJLTtNVPVgV+ib8OMANTu416IyL9h2DVkx/5vjpn3M8DTFBwsrgHQSh2Yy K2LUKzCYkPDjCCjidXBwoacl3w79prP+1+4rT8BTYzKz5tC7VMHyVh2tkj2lVhdS HigZrKf0F0m/4fqxPcG+lYYCLhsFfrS+5n4YfJ4t1Urc6ZU+QpiyOkhehA/fggdz ujdiv/G7dPa9iTcWCLz/fzf/RygdNKFyHtt0K4EaaJQlV/fCzWIwYQGpeJQiwcry 35D3t6OPrqp3POafRPVsLw/SKM0+60WcnOIWRKzP/fDm+ylmFxT5zmOqCv45TysH aOa0nOy9qMGfs9W29p8MGFgpkuro0F3n2ZL5Zq6UnqSIUpOmkctBm4gA1vF0wFHv 5H5tdzPfBWfzVjssJCHmNHadjfWbGaG1NN6AqQyyCNXB6y8oSOh87f/zwJeV1g/I cEe+JKAV3D3k7aoYrftdmJtlxEKdiq27L1jrJzI+QoImXrzejd4= =QKuy -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 03 16:44:03 2025 Received: (at 75920-done) by debbugs.gnu.org; 3 Feb 2025 21:44:03 +0000 Received: from localhost ([127.0.0.1]:41626 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tf4Ec-0001v4-Mi for submit@debbugs.gnu.org; Mon, 03 Feb 2025 16:44:03 -0500 Received: from mx2.dismail.de ([159.69.191.136]:18947) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tf4EZ-0001uM-Jv for 75920-done@debbugs.gnu.org; Mon, 03 Feb 2025 16:44:00 -0500 Received: from mx2.dismail.de (localhost [127.0.0.1]) by mx2.dismail.de (OpenSMTPD) with ESMTP id 58f59d37; Mon, 3 Feb 2025 22:43:52 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed; d=dismail.de; h=from:to:cc :subject:in-reply-to:date:message-id:mime-version:content-type; s=20190914; bh=4hiOjj6t0DfInYQDslKFdadLcrDmbdW7gIjVuh7Vg2o=; b= ZKspwAImGnjUPL7W3fcumRzRECQr8gKyN27/1UGrG3/7A9x8dolXkRVTW2ipXhAR FkWP1HbccGlGHNl0pDqFhQqQ1fJFFW1sTNBgMP01HX5hnCTyHx3L7yzCNzRsf/0h aiZMx9AehvkYGi/xF0j1rrk3GnvbUSPBJSzFJw6uMp1tET4Tji/Tdy4wSsr0vet4 bU3A069iX8Parokk+nQniABPlrUzc7mwg6z/q7lwM+2dYAkjK8R0MmMR4bBHNSkY 1mLuQAtvOEePPm4lAXWbttvP4cGX4ztNmr5TXU7NIH8nEoWrZjtDf8Lo0Dt+pO4/ +kxTAtL0cRJGcbT5mI3w3A== Received: from smtp2.dismail.de ( [10.240.26.12]) by mx2.dismail.de (OpenSMTPD) with ESMTP id b67744f0; Mon, 3 Feb 2025 22:43:52 +0100 (CET) Received: from smtp2.dismail.de (localhost [127.0.0.1]) by smtp2.dismail.de (OpenSMTPD) with ESMTP id 8f86d22a; Mon, 3 Feb 2025 22:43:52 +0100 (CET) Received: by dismail.de (OpenSMTPD) with ESMTPSA id 1998f858 (TLSv1.3:TLS_AES_256_GCM_SHA384:256:NO); Mon, 3 Feb 2025 22:43:51 +0100 (CET) From: jgart To: 75920-done@debbugs.gnu.org Subject: Re: [PATCH] gnu: Add ravanan. In-Reply-To: <87y0ymkbun.fsf@gmail.com> Date: Mon, 03 Feb 2025 16:43:48 -0500 Message-ID: <87tt9a7lgr.fsf@dismail.de> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 75920-done Cc: Arun Isaac , Sharlatan Hellseher X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) > I CC Guile user to verify some other build formating otions. > > For some reason we have no guile team ^.- Hi Oleg, Oops I missed your message. This patch is already applied. Arun, Feel free to open a new ticket if you need to add more build formatting option suggestions. -- all the best, jgart From debbugs-submit-bounces@debbugs.gnu.org Sun Feb 09 07:00:06 2025 Received: (at 75920-done) by debbugs.gnu.org; 9 Feb 2025 12:00:07 +0000 Received: from localhost ([127.0.0.1]:43431 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1th5yo-0006HL-IL for submit@debbugs.gnu.org; Sun, 09 Feb 2025 07:00:06 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:55672) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1th5yk-0006Fi-KY for 75920-done@debbugs.gnu.org; Sun, 09 Feb 2025 07:00:05 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=systemreboot.net; s=default; t=1739102394; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: in-reply-to:in-reply-to:references:references; bh=Et2xj9N++rfx0cGYtT/2oksjtIlrXKbNzLgb40jYunc=; b=G5OxturdND0W3jQMY6YBDM673jm5W6EytN1+tCUBGlC7HYTDDd/8nFDKtGYf6SW+qvHfzG E3Dep9Xh/9UUBljdi+J6vwRvI1dbyYN23Ggbj/6seDdwhqPyFANuEOfeoKHsY32X6K2QN6 DRdA4A2U08SNlf7iPsGVl5BCp80z1l6gocFVR9VDviyVJj+owco0AfYeOalA6bb9zsHqTS G/qUTkyxSCI7bzuH+PvYd2PU2g2cW8tPQpYBIQa7Xomj1O/CWamEh+3TfUNCwSv8Xnol4d kWZdz106zTKfOtjxwUgEnsapcFpg5iDGDRLvXBdlWTYovWEmX6c8JN9rN2yyrQ== Received: from localhost ( [192.168.2.1]) by mugam.systemreboot.net (OpenSMTPD) with ESMTPSA id d42a8077 (TLSv1.3:TLS_AES_256_GCM_SHA384:256:NO); Sun, 9 Feb 2025 11:59:53 +0000 (UTC) From: Arun Isaac To: jgart , 75920-done@debbugs.gnu.org Subject: Re: [PATCH] gnu: Add ravanan. 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