From mboxrd@z Thu Jan 1 00:00:00 1970 From: Marius Bakke Subject: Re: [PATCH 3/4] gnu: Add barrnap. Date: Sat, 03 Dec 2016 20:36:04 +0100 Message-ID: <87twakbyaj.fsf@kirby.i-did-not-set--mail-host-address--so-tickle-me> References: <20161203103901.27770-1-donttrustben@gmail.com> <20161203103901.27770-3-donttrustben@gmail.com> Mime-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:44968) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cDG6X-0000ey-5p for guix-devel@gnu.org; Sat, 03 Dec 2016 14:36:14 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cDG6U-0001Za-1E for guix-devel@gnu.org; Sat, 03 Dec 2016 14:36:13 -0500 Received: from out5-smtp.messagingengine.com ([66.111.4.29]:34569) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cDG6T-0001ZQ-RM for guix-devel@gnu.org; Sat, 03 Dec 2016 14:36:09 -0500 In-Reply-To: <20161203103901.27770-3-donttrustben@gmail.com> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Ben Woodcroft , guix-devel@gnu.org --=-=-= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable Ben Woodcroft writes: > * gnu/packages/bioinformatics.scm (barrnap): New variable. > --- > gnu/packages/bioinformatics.scm | 67 +++++++++++++++++++++++++++++++++++= ++++++ > 1 file changed, 67 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm > index 961f0b2..4541791 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -268,6 +268,73 @@ instance, it implements several methods to assess co= ntig-wise read coverage.") > BAM files.") > (license license:expat))) >=20=20 > +(define-public barrnap > + (package > + (name "barrnap") > + (version "0.7") > + (source > + (origin > + (method url-fetch) > + (uri (string-append > + "https://github.com/tseemann/barrnap/archive/" > + version ".tar.gz")) > + (file-name (string-append name "-" version ".tar.gz")) > + (sha256 > + (base32 > + "16y040np76my3y82hgk4yy790smbsk4h8d60d5swlv7ha3i768gg")) > + (modules '((guix build utils))) > + ;; Remove pre-built binaries. > + (snippet '(begin > + (delete-file-recursively "binaries") > + #t)))) > + (build-system gnu-build-system) > + (arguments > + `(#:test-target "test" > + #:phases > + (modify-phases %standard-phases > + (add-after 'unpack 'patch-nhmer-path > + (lambda* (#:key inputs #:allow-other-keys) > + (substitute* "bin/barrnap" > + (("^my \\$NHMMER =3D .*") > + (string-append "my $NHMMER =3D '" > + (assoc-ref inputs "hmmer") > + "/bin/nhmmer';\n"))) > + #t)) > + (delete 'configure) > + (delete 'build) > + (replace 'install > + (lambda* (#:key outputs #:allow-other-keys) > + (let* ((out (assoc-ref outputs "out")) > + (bin (string-append out "/bin")) > + ;(path (getenv "PATH")) > + (share (string-append out "/share/barrnap/db")) > + (binary "bin/barrnap")) > + (substitute* binary > + (("^my \\$DBDIR =3D .*") > + (string-append "my $DBDIR =3D '" share "';\n"))) > + (install-file binary bin) > + (mkdir-p share) > + (copy-recursively "db" share)) > + #t))))) > + (inputs > + `(("perl" ,perl) > + ("hmmer" ,hmmer))) > + (home-page "https://github.com/tseemann/barrnap") > + (synopsis "Ribosomal RNA predictor") > + (description > + "Barrnap predicts the location of ribosomal RNA genes in genomes. It > +supports bacteria (5S, 23S, 16S), archaea (5S,5.8S,23S,16S), mitochondri= a (12S, > +16S) and eukaryotes (5S, 5.8S, 28S, 18S). It takes FASTA DNA sequence a= s input, > +and write GFF3 as output. It uses the NHMMER tool that comes with HMMER= for > +HMM searching in RNA:DNA style.") > + (license (list license:gpl3 > + ;; The Rfam HMMs are under cc0, and the SILVA-derived = HMMs are > + ;; academic-only. I don't think we can package the SILVA files. They are very much non-free according to the license text: SILVA Terms of Use/License Information The SILVA database content offered at www.arb-silva.de can be freely browsed and the corresponding information deployed by all users, independent from their status (academic or non-academic). All downloads are free for academic users. They can be used, modified and redistributed within the academic environment without any limitation. However, in case of redistribution please make transparent the SILVA Terms of Use/License Information by linking/referring to this page (see link in the header of your browser). Academic users are represented by universities and non-commercial research institutes such as members of the German Helmholtz Association, Leibniz Association and Max-Planck Society as well as US National Labs. Users from NON-ACADEMIC can also directly access all downloads including the results of the SILVA web-aligner (SINA) but only for limited/temporary use (only for test purposes). All downloaded files should be deleted latest after 48 hours. Unauthorized usage beyond test purposes is strictly prohibited. If you are interested in unlimited usage of the SILVA databases/services (e.g. the web-aligner) or parts of them within a non-academic environment, please contact us for more information at contact(at)arb-silva.de. A non-academic environment is defined by a direct or indirect commercial interest in the data and includes all industrial research entities. > + license:cc0 > + (license:non-copyleft > + "file:///LICENSE.SILVA" > + "See LICENSE.SILVA in the distribution."))))) > + > (define-public bcftools > (package > (name "bcftools") > --=20 > 2.10.2 --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEu7At3yzq9qgNHeZDoqBt8qM6VPoFAlhDHqQACgkQoqBt8qM6 VPrIdQf+O7Eef4mygg+8ZeDygonzExQhZG3O5jFeRHT3MDrTzMpg/llDCOk8vO/O MiR+1HQFQyS3YKd7iYrpdG5f8GFaVScxcHJpUyZuraZoHttqrB+X0ByTKejEpEBy 595uCtpwKviD3SVulv+wBrU9HZYmeCXoFXhakh/EKpSzIwAY47gcNXTOClfaDPIN Nbf1vJ2kXuXUT+G3fIvX/3gsdeybSGo0e55hweApuqhJk5MLRYPkNPfApU678/Uy ZhVce9KPRsywBiLoYhMGr7WCaRy3KYGX3PQJtqroxzd0KF43IzYrADP98fhIcEVH I7l+9Iqao+kW6QJMMAfUTj1TSxznMw== =Jw4x -----END PGP SIGNATURE----- --=-=-=--