From mboxrd@z Thu Jan 1 00:00:00 1970 From: Efraim Flashner Subject: Re: [PATCH] gnu: Add Infernal. Date: Mon, 5 Sep 2016 12:32:08 +0300 Message-ID: <20160905093208.GD23794@macbook42.flashner.co.il> References: <20160902133514.26930-1-ricardo.wurmus@mdc-berlin.de> Mime-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="T6xhMxlHU34Bk0ad" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:34604) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bgqGM-0004tH-Am for guix-devel@gnu.org; Mon, 05 Sep 2016 05:32:26 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bgqGI-0007wz-02 for guix-devel@gnu.org; Mon, 05 Sep 2016 05:32:22 -0400 Received: from flashner.co.il ([178.62.234.194]:57795) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bgqGH-0007un-M6 for guix-devel@gnu.org; Mon, 05 Sep 2016 05:32:17 -0400 Content-Disposition: inline In-Reply-To: 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: Ricardo Wurmus Cc: guix-devel --T6xhMxlHU34Bk0ad Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Fri, Sep 02, 2016 at 04:12:21PM +0200, Ricardo Wurmus wrote: >=20 > Thompson, David writes: >=20 > > On Fri, Sep 2, 2016 at 9:35 AM, Ricardo Wurmus > > wrote: > >> * gnu/packages/bioinformatics.scm (infernal): New variable. > >> --- > >> gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ > >> 1 file changed, 27 insertions(+) > >> > >> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinforma= tics.scm > >> index 08c2545..1652f71 100644 > >> --- a/gnu/packages/bioinformatics.scm > >> +++ b/gnu/packages/bioinformatics.scm > >> @@ -4835,6 +4835,33 @@ data in the form of VCF files.") > >> ;; at https://vcftools.github.io/license.html > >> (license license:lgpl3))) > >> > >> +(define-public infernal > >> + (package > >> + (name "infernal") > >> + (version "1.1.2") > >> + (source (origin > >> + (method url-fetch) > >> + ;; There are no versioned tarballs > > > > But the version appears in the URL? >=20 > Sorry, this comment was supposed to be removed before sending out the > patch. Noticed it too late. >=20 > >> + (uri (string-append "http://eddylab.org/software/infern= al/" > >> + "infernal-" version ".tar.gz")) > >> + (sha256 > >> + (base32 > >> + "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c= ")))) > >> + (build-system gnu-build-system) > >> + (native-inputs > >> + `(("perl" ,perl))) ; for tests > >> + (home-page "http://eddylab.org/infernal/") > >> + (synopsis "Inference of RNA alignments") > >> + (description "Infernal (\"INFERence of RNA ALignment\") is a tool= for > >> +searching DNA sequence databases for RNA structure and sequence simil= arities. > >> +It is an implementation of a special case of profile stochastic conte= xt-free > >> +grammars called @dfn{covariance models} (CMs). A CM is like a sequen= ce > >> +profile, but it scores a combination of sequence consensus and RNA se= condary > >> +structure consensus, so in many cases, it is more capable of identify= ing RNA > >> +homologs that conserve their secondary structure more than their prim= ary > >> +sequence.") > >> + (license license:bsd-3))) > >> + > >> (define-public r-vegan > >> (package > >> (name "r-vegan") > >> -- > >> 2.9.3 > >> > >> > > > > LGTM overall. >=20 > Okay, will push in a moment (after removing the wrong comment). > Thanks for taking a look! >=20 > ~~ Ricardo >=20 After checking the hydra logs I removed support for armhf and mips, since they lack the necessary hardware features to build the package. --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --T6xhMxlHU34Bk0ad Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iQIcBAEBCgAGBQJXzTuYAAoJEPTB05F+rO6TtBoP/25zvNUETGdGxKhN+r72n708 j1/avGQ9mOUAKVSuioRyMSrsTKqkQHvWbIZJ+vnBSMhRqupW8vkR20zrUbDd21mt ++ATfjxklkbljWwFDPzwPk7ObjPvv7WmlI16DCPKlq6SrQ47EUJDpDsGsv8MwQLq nxlICe2cvNrDaJE/mVyzFvi3Y1fUsx707NudIH/mtL7L/hgsDz4tY8/fCeTHtMV3 iQMhGnITUw1lI3RYIr+VqDx6pRFTOz+wg28vclEpDfrhZd116HLiz+o7vOR6wSO0 0dJTck70D/UrQ6BajkIvo+Ih5z/npyBvRRh9UsHJz/SDwH5hUncwktIGWqyLkku/ kfVCdrC5TgkGvddveY0GRXzSKbJF6A6F38pyh39Wuo3pkB9c+/9x/Kf2OdrhT0Dc /osvxS4boGMVt1Ew3GFkA9iBB2xBwskdKVgQH1iYaBy8vIwS1ERDAithEdGarJv3 lFpWoENe/uwGi7v+ZHZmijc2WZscuI8df/zqGgRN97b6Ultue6i3gWPsE0nGMqAZ RzBr7FPW3pfcDkRZUlvCiGr6gQ/AmIdg5Owphf06CCl3w73DTXFdtqw8LVHg/1h6 fQ1LoTVxxM+8c7/UzzV1yh7TOv7jWUofY329K02ZvDYCIeKReICUpK37w6gBb+R4 Ahsy0T6EwIyO8VzjU/a4 =bsZI -----END PGP SIGNATURE----- --T6xhMxlHU34Bk0ad--