From unknown Fri Jun 20 07:20:20 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#32781 <32781@debbugs.gnu.org> To: bug#32781 <32781@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add poretools. Reply-To: bug#32781 <32781@debbugs.gnu.org> Date: Fri, 20 Jun 2025 14:20:20 +0000 retitle 32781 [PATCH] gnu: Add poretools. reassign 32781 guix-patches submitter 32781 pimi severity 32781 normal tag 32781 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Thu Sep 20 06:23:52 2018 Received: (at submit) by debbugs.gnu.org; 20 Sep 2018 10:23:52 +0000 Received: from localhost ([127.0.0.1]:46354 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g2w7k-0005cH-5a for submit@debbugs.gnu.org; Thu, 20 Sep 2018 06:23:52 -0400 Received: from eggs.gnu.org ([208.118.235.92]:36151) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g2w7h-0005c4-UC for submit@debbugs.gnu.org; Thu, 20 Sep 2018 06:23:50 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1g2w7a-0003k5-V3 for submit@debbugs.gnu.org; Thu, 20 Sep 2018 06:23:44 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,T_DKIM_INVALID autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:48153) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1g2w7a-0003jN-Ko for submit@debbugs.gnu.org; Thu, 20 Sep 2018 06:23:42 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:57053) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1g2w7Y-0005XC-DB for guix-patches@gnu.org; Thu, 20 Sep 2018 06:23:42 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1g2w7V-0003cB-0D for guix-patches@gnu.org; Thu, 20 Sep 2018 06:23:40 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:41650) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1g2w7S-0003M8-QM for guix-patches@gnu.org; Thu, 20 Sep 2018 06:23:36 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 520BDAE44AF for ; Thu, 20 Sep 2018 12:23:27 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:x-mailer:message-id:date :date:subject:subject:from:from:received:received:received; s= mdc; t=1537439001; x=1539253402; bh=5MAkczdn5F3d85Kc6/Yk0rhj0AXp k5aoqzZshmq1XvI=; b=GidW1crjRmvdPLUAyhdysXEeqdhhk3szyczT0+zKRyZV YhsJNVnW4z4lzvtl5l2l3IKmfgCfZavVT4+lvOM27h92nq7KJdsM9+zX43uzG+eo UHV2098/zZI83hmwRGMMTU5tWNA72ww+jRn0QOGoW0UBWqKeAQTkhjcB9f8pmLA= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id eQnbI9Vf9C-0 for ; Thu, 20 Sep 2018 12:23:21 +0200 (CEST) Received: from SW-IT-P-CAS3.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Thu, 20 Sep 2018 12:23:21 +0200 (CEST) Received: from biadmin-KVM.nat (141.80.113.106) by SW-IT-P-CAS3.mdc-berlin.net (141.80.113.58) with Microsoft SMTP Server (TLS) id 14.3.408.0; Thu, 20 Sep 2018 12:23:21 +0200 From: pimi To: Subject: [PATCH] gnu: Add poretools. Date: Thu, 20 Sep 2018 12:22:58 +0200 Message-ID: <20180920102258.17005-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24106.005 X-TM-AS-Result: No-5.659900-8.000000-10 X-TMASE-MatchedRID: sCy2GwBQH7x7qToVEfwBPAPZZctd3P4Bc3ewuwbSaG41LB46LFAAkrDW HFry+EP42hmlV4QMClrxlv0JrxO0ztA4NqdM7aY0i3TrOhAURKEt0t+aIVLt+w2Y8xyy93kWkA/ oON3vcwDI4b5i74dtIS0pUKEDgMS9GNZpatR+Wd6sgaPSWrovRgreImldQ5BDBMVCd71wdDqjxY yRBa/qJV/Hpl/zcOjl6WhiDOOieuzKayT/BQTiGs99eFQxdtTGY9yeq0CNdXnB0vjh1zVuR/uN8 op0sPc2PghwFVaNEpMd5c1LIJsPCVP1x1IptQJ1j5W5x58BQZ2ainaOvy7pGYs6mgIqcRHBXyZ6 pl/oDQ1+Az0rNWZh1oK3xHwHujePaS3XXfcxpZY= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.659900-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24106.005 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.3 (----) X-Debbugs-Envelope-To: submit Cc: pimi 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: -5.3 (-----) * gnu/packages/bioinformatics.scm (poretools): New variable. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 67f24a617..fdc35e684 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13723,3 +13723,42 @@ juicer) and single-resolution or multi-resolution @code{.cool} files (for cooler). Both @code{hic} and @code{cool} files describe Hi-C contact matrices.") (license license:expat))) + +(define-public poretools + ;; The latest release was in 2016 and the latest commit is from 2017 + ;; the recommended way to install is to clone the git repository + ;; https://poretools.readthedocs.io/en/latest/content/installation.html + (let ((commit "e426b1f09e86ac259a00c261c79df91510777407") + (revision "1")) + (package + (name "poretools") + (version (git-version "0.6.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/arq5x/poretools.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am")))) + (build-system python-build-system) + ;; requires python >=2.7, <3.0, and the same for python dependencies + (arguments `(#:python ,python-2)) + (inputs + `(("hdf5" ,hdf5))) + (propagated-inputs + `(("python-dateutil" ,python2-dateutil) + ("python-h5py" ,python2-h5py) + ("python-matplotlib" ,python2-matplotlib) + ("python-pandas" ,python2-pandas) + ("python-seaborn" ,python2-seaborn))) + (home-page "https://poretools.readthedocs.io") + (synopsis "Toolkit for working with nanopore sequencing data") + (description + "The MinION from Oxford Nanopore Technologies is a nanopore sequencer. +This @code{poretools} package is a flexible toolkit for exploring datasets +generated by nanopore sequencing devices for the purposes of quality control and +downstream analysis. Poretools operates directly on the native FAST5, a variant +of the Hierarchical Data Format (HDF5) standard.") + (license license:expat)))) -- 2.17.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 02 16:05:48 2018 Received: (at 32781-done) by debbugs.gnu.org; 2 Oct 2018 20:05:48 +0000 Received: from localhost ([127.0.0.1]:34674 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g7QvU-0002C9-0w for submit@debbugs.gnu.org; Tue, 02 Oct 2018 16:05:48 -0400 Received: from wnew1-smtp.messagingengine.com ([64.147.123.26]:56155) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g7QvR-0002C1-OH for 32781-done@debbugs.gnu.org; Tue, 02 Oct 2018 16:05:46 -0400 Received: from compute4.internal (compute4.nyi.internal [10.202.2.44]) by mailnew.west.internal (Postfix) with ESMTP id D324E926; Tue, 2 Oct 2018 16:05:44 -0400 (EDT) Received: from mailfrontend1 ([10.202.2.162]) by compute4.internal (MEProxy); Tue, 02 Oct 2018 16:05:45 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=cc:content-type:date:from:in-reply-to:message-id:mime-version :references:subject:to:x-me-sender:x-me-sender:x-sasl-enc; s= mesmtp; bh=Ym+yMfxvRLVkeCkzE2cvBU4AXVa7qsZdJdZXCnneZaM=; b=Q0gXD WvGyI14o1tjQpmJq8CPIpuNv8n89eWylOiQD/kuYoI0K4XLm/ihW10258Q/ZGB2Z VY2oXS6vfcVDLZaOTIg/G4VhAdRSlvdys5l5uRBCtEChqWVLTowWhuJZG2G/4Qtp IuN71p+vuok5oIZIn+XT6ULXnuimv+UiM3+Q+s= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:from:in-reply-to :message-id:mime-version:references:subject:to:x-me-sender :x-me-sender:x-sasl-enc; s=fm3; bh=Ym+yMfxvRLVkeCkzE2cvBU4AXVa7q sZdJdZXCnneZaM=; b=OswsmyxCgRqUsTstwww+S3GqDdKQDm/k9Wgm2vwFd4Vs0 LxwX3KA5ZtDw25chaMCIcSpxdo0C2aN/QvlyN2MjZdv+hk//mcb1yIEyfObaHX04 ss3PISyn2E1V4ALhmLjn2nu8aLh1WJYGliaUcmiGFAVtlkMfN4wQv3rWLLiKagJ6 Mk6u4Qdgh6YeLCAscmVaQsUcb/Ur29dZCXqjl56pwtn81hVXQ7zGSiw12rsOzyZ7 MOJfgkpvBaUTY9TuQu/ZIydcAjMWA26xYMoc+NvFqaW3lMJBKUTWPy6GDvByl41r NuxzhBsyeOnkwwmZzloHVxGdj/V3KEPC2Y3k8dSNw== X-ME-Sender: X-ME-Proxy: Received: from localhost (unknown [172.58.201.36]) by mail.messagingengine.com (Postfix) with ESMTPA id E4558E4A3C; Tue, 2 Oct 2018 16:05:43 -0400 (EDT) Date: Tue, 2 Oct 2018 16:05:42 -0400 From: Leo Famulari To: pimi Subject: Re: [bug#32781] [PATCH] gnu: Add poretools. Message-ID: <20181002200542.GC18113@jasmine.lan> References: <20180920102258.17005-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="m51xatjYGsM+13rf" Content-Disposition: inline In-Reply-To: <20180920102258.17005-1-madalinionel.patrascu@mdc-berlin.de> User-Agent: Mutt/1.10.1 (2018-07-13) X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 32781-done Cc: 32781-done@debbugs.gnu.org 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: -1.7 (-) --m51xatjYGsM+13rf Content-Type: text/plain; charset=us-ascii Content-Disposition: inline On Thu, Sep 20, 2018 at 12:22:58PM +0200, pimi wrote: > * gnu/packages/bioinformatics.scm (poretools): New variable. Thank you! Pushed as 3f0f49d70877df6c829b443830de99e0e1e1f6bc --m51xatjYGsM+13rf Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCAAdFiEEsFFZSPHn08G5gDigJkb6MLrKfwgFAluzz5YACgkQJkb6MLrK fwjB/w//W/fzPoloJqJApVsNWYglEMVxDWL3qVaNwotWJKeJqQ55qJA4hMIP2N8o TIwYkBuP5Y79HrEK02kL0Mc2rWnYdyUjr8TuF4iVsSjzMgl+7QdDQZGhvdGOuO0f ne+6vsmmh4IOdv49duUdTyDdlit4unXk7vb+JxZyqw/7/XMaw5V+oPiX4jK6eZ9z YnJbEauVR6XC9BLWhq9KoDhuTb+gy+dDYZZdLGg976NvmesGVOPiclqGTT3R8rnr dnxGCWSJxE/rJ3QWFbyeMm91qi2fhT87isPZ+ZYrXBQuE8vwwD1S0zsaMjq018dj mkp1dVL9wSNqgDyXOQKU+2OEh2wJlhgJe44vxaL89G06JSy5xl0dMcir7OPjdrZe DVmFLmOCk0BwmKltpe/1YaJ9yHSb+gyusaG7RVnV1rw+cLHlWZMSeocyLsWkDZ9t AejiOebzD2kzFoaFU6EkFkHqStAhEUJ4hCzTL9r1H82LSvtyS9bhWeC4TB4iloj6 B9zduaQydoFciCizNoM2MiW74uR/tjRblE1hhZPHOFEfepr3SFbif8FGSdftbA/s q8yk21B6C1LaHoEJ8xQCQzB+WDBBYhK/rqVmpFLAT2nVWz5SoSjWvrzbcrHZDQaU 9/Cwy/WESACwhiRDgpsJI0Ll7b6io9IE+a3Hj06KwlHRNf0ShBo= =snym -----END PGP SIGNATURE----- --m51xatjYGsM+13rf-- From unknown Fri Jun 20 07:20:20 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Wed, 31 Oct 2018 11:24:07 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator