From mboxrd@z Thu Jan 1 00:00:00 1970 From: Marius Bakke Subject: Re: [PATCH 2/4] gnu: Add ncbi-tools. Date: Sat, 03 Dec 2016 20:30:04 +0100 Message-ID: <87wpfgbykj.fsf@kirby.i-did-not-set--mail-host-address--so-tickle-me> References: <20161203103901.27770-1-donttrustben@gmail.com> <20161203103901.27770-2-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]:44411) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cDG0h-0008HY-38 for guix-devel@gnu.org; Sat, 03 Dec 2016 14:30:12 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cDG0d-0007tK-V8 for guix-devel@gnu.org; Sat, 03 Dec 2016 14:30:11 -0500 Received: from out5-smtp.messagingengine.com ([66.111.4.29]:42165) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cDG0d-0007rK-NI for guix-devel@gnu.org; Sat, 03 Dec 2016 14:30:07 -0500 In-Reply-To: <20161203103901.27770-2-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 (ncbi-tools): New variable. > --- > gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++++= ++++++ > 1 file changed, 62 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm > index 415024f..961f0b2 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -80,6 +80,7 @@ > #:use-module (gnu packages readline) > #:use-module (gnu packages ruby) > #:use-module (gnu packages serialization) > + #:use-module (gnu packages shells) > #:use-module (gnu packages statistics) > #:use-module (gnu packages tbb) > #:use-module (gnu packages tex) > @@ -4340,6 +4341,67 @@ simultaneously.") > ("ngs-sdk" ,ngs-sdk))) > (synopsis "Java bindings for NGS SDK"))) >=20=20 > +(define-public ncbi-tools > + (package > + (name "ncbi-tools") > + (version "20160908") > + (source > + (origin > + (method url-fetch) > + (uri (string-append "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ol= d/" > + version "/ncbi.tar.gz")) I'm getting a timeout on this, though it works in a browser. However this server is apparently also available over HTTPS, which is better. > + (file-name (string-append name "-" version ".tar.gz")) > + (sha256 > + (base32 > + "1252s4fw41w5yalz9b50pvzvkiyjfcgy0isw1qgmg0v66bp49khz")))) > + (build-system gnu-build-system) > + (arguments > + `(#:tests? #f ; There are no tests. > + #:phases > + (modify-phases %standard-phases > + (delete 'configure) > + (add-after 'unpack 'patch-sources > + (lambda _ > + (for-each (lambda (file) > + (substitute* file > + (("NCBI_MAKE_SHELL =3D .*") > + (string-append > + "NCBI_MAKE_SHELL =3D " > + (which "sh") > + "\n")))) > + (find-files "platform" ".*mk")) > + (substitute* "make/ln-if-absent" > + (("set path=3D\\(/usr/bin /bin\\)") "")) > + #t)) > + (replace 'build > + (lambda _ > + (chdir "..") > + (zero? (system* "ncbi/make/makedis.csh")))) > + (replace 'install > + (lambda* (#:key outputs #:allow-other-keys) > + (let* ((out (assoc-ref outputs "out")) > + (bin (string-append out "/bin")) > + (man (string-append out "/share/man/man1"))) > + (for-each (lambda (file) > + (install-file > + (string-append "ncbi/build/" file) bin) > + (install-file > + (string-append "ncbi/doc/man/" file ".1") ma= n)) > + ;; XXX: TODO: Install and test other binaries. > + (list "tbl2asn")) > + #t)))))) > + (native-inputs > + `(("csh" ,tcsh) > + ("pkg-config" ,pkg-config) > + ("coreutils" ,coreutils))) > + (home-page "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.= html") > + (synopsis "NCBI-related tools") > + (description "The United States of America @dfn{National Center for > +Biotechnology Information} (NCBI) Software Development Toolkit is for the > +production and distribution of GenBank, Entrez, BLAST and related NCBI > +services.") > + (license license:public-domain))) The files in regexp/ are released under a custom license found in regexp/doc/LICENSE. Also corelib/regex.{c.h} are GPL2+. algo/blast/core/boost_erf.c is covered by boost1.0, and connect/parson.{c,h} are MIT. Some files in connect/mitsock seems to be covered by an early variant of the 2-clause BSD. Other files have unclear license terms such as those in corelib/morefiles, though they seem sufficiently free for the non-copyleft procedure. LGTM with these updates! > + > (define-public ncbi-vdb > (package > (name "ncbi-vdb") > --=20 > 2.10.2 --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEu7At3yzq9qgNHeZDoqBt8qM6VPoFAlhDHTwACgkQoqBt8qM6 VPqY8wf/Xd3Zp3P/uGynshRlFxZiJ/rmDzNVgFy9ekxH97iJExwlEzvGTOY76nhQ L7BnoWBzBJpmZE+Je4Gc+3Z1sew/pzwV1OrnUJ+NAINc+CK2Xga7cybhehSfmbQf rt+Z5QE+kqhXYq4V76XsRAcXHqIaXM1P42NdG6/dm1DFC2oiZigSjdtKSUsBAa/L Ycaz8PDuJJKhUrWxhWxYtXHH4VYdgEa3Fk4byps2d7N9hDrxj/7GZvV2lFCLVs+t PGc+4B/MmH4BmDUzbei7nbRgfLamIDMIYe8jmaEUQo/ZhQY/s7wWeW5CDBiBb+5J Dh3Dz6rYRYinfd3PHKZu2LTojcNGiQ== =MKPd -----END PGP SIGNATURE----- --=-=-=--