From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH 2/4] gnu: Add ncbi-tools. Date: Sat, 3 Dec 2016 20:38:59 +1000 Message-ID: <20161203103901.27770-2-donttrustben@gmail.com> References: <20161203103901.27770-1-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:50339) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cD7iy-0000lP-I1 for guix-devel@gnu.org; Sat, 03 Dec 2016 05:39:21 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cD7iw-0006A4-Es for guix-devel@gnu.org; Sat, 03 Dec 2016 05:39:20 -0500 Received: from mail-pg0-x244.google.com ([2607:f8b0:400e:c05::244]:32823) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1cD7iw-00069x-6F for guix-devel@gnu.org; Sat, 03 Dec 2016 05:39:18 -0500 Received: by mail-pg0-x244.google.com with SMTP id 3so10545261pgd.0 for ; Sat, 03 Dec 2016 02:39:18 -0800 (PST) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id o68sm13952132pfb.42.2016.12.03.02.39.13 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Sat, 03 Dec 2016 02:39:14 -0800 (PST) In-Reply-To: <20161203103901.27770-1-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: guix-devel@gnu.org * 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/bioinformatics.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"))) +(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/old/" + version "/ncbi.tar.gz")) + (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 = .*") + (string-append + "NCBI_MAKE_SHELL = " + (which "sh") + "\n")))) + (find-files "platform" ".*mk")) + (substitute* "make/ln-if-absent" + (("set path=\\(/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") man)) + ;; 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))) + (define-public ncbi-vdb (package (name "ncbi-vdb") -- 2.10.2