From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] Add FastTree Date: Sat, 20 Jun 2015 15:32:41 +1000 Message-ID: <5584FAF9.8090902@uq.edu.au> References: <5583C3A2.1080906@uq.edu.au> <87oakcqa4r.fsf@gmail.com> <55849800.30201@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------030509030409090301040709" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:34125) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z6BOf-0002ZI-25 for guix-devel@gnu.org; Sat, 20 Jun 2015 01:32:54 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z6BOb-0001BC-Rg for guix-devel@gnu.org; Sat, 20 Jun 2015 01:32:52 -0400 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:54060 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z6BOb-0001B3-8G for guix-devel@gnu.org; Sat, 20 Jun 2015 01:32:49 -0400 In-Reply-To: <55849800.30201@uq.edu.au> 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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Alex Kost Cc: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------030509030409090301040709 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit On 20/06/15 08:30, Ben Woodcroft wrote: > On 19/06/15 20:13, Alex Kost wrote: >> Ben Woodcroft (2015-06-19 10:24 +0300) wrote: >> >>> Hi, >> Hi, I didn't try your patch, so I don't have real comments, just some >> general cosmetic notes, if you don't mind. > Thanks, all help appreciated. Updated patch attached. Sorry now without the extraneous files. --------------030509030409090301040709 Content-Type: text/x-patch; name="0001-gnu-Add-fasttree.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-fasttree.patch" >From af17052d0f613ba53c7bc14fb99e143a60f97713 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 20 Jun 2015 15:30:42 +1000 Subject: [PATCH] gnu: Add fasttree * gnu/packages/bioinformatics.scm (fasttree): New variable. --- gnu/packages/bioinformatics.scm | 61 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 12c9175..fb701f9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -34,6 +34,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages file) + #:use-module (gnu packages gcc) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages machine-learning) @@ -780,6 +781,66 @@ analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.") (license license:artistic2.0))) +(define-public fasttree + (package + (name "fasttree") + (version "2.1.8") + (source (origin + (method url-fetch) + (uri (string-append + "http://www.microbesonline.org/fasttree/FastTree-" + version ".c" + )) + (sha256 + (base32 + "0dzqc9vr9iiiw21y159xfjl2z90vw0y7r4x6456pcaxiy5hd2wmi")))) + (build-system trivial-build-system) + (arguments + '(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils) (system base compile)) + (let ((source (assoc-ref %build-inputs "source")) + (gcc (assoc-ref %build-inputs "gcc")) + (glibc (assoc-ref %build-inputs "glibc")) + (binutils (assoc-ref %build-inputs "binutils")) + (out (assoc-ref %outputs "out"))) + (setenv "PATH" (string-append binutils "/bin:" gcc "/bin")) + (setenv "LIBRARY_PATH" (string-append glibc "/lib")) + (let ((bin (string-append out "/bin"))) + (mkdir-p bin) + (system* "gcc" + "-O3" + "-finline-functions" + "-funroll-loops" + "-Wall" + "-o" + (string-append bin "/FastTree") + source + "-lm") + (system* "gcc" + "-DOPENMP" + "-fopenmp" + "-O3" + "-finline-functions" + "-funroll-loops" + "-Wall" + "-o" + (string-append bin "/FastTreeMP") + source + "-lm")))))) + (native-inputs + `(("gcc", gcc-5.1) + ("binutils" ,binutils) + ("glibc" ,glibc))) + (home-page "http://www.microbesonline.org/fasttree") + (synopsis "Infers approximately-maximum-likelihood phylogenetic trees") + (description + "FastTree can handle alignments with up to a million of sequences in +a reasonable amount of time and memory. For large alignments, FastTree is +100-1,000 times faster than PhyML 3.0 or RAxML 7.") + (license license:gpl2+))) + (define-public fastx-toolkit (package (name "fastx-toolkit") -- 2.1.4 --------------030509030409090301040709--