New upstream version 1.7.2+dfsg

            -I$(CURDIR)/../genometools/src/external/zlib-1.2.8 \

            -I$(CURDIR)/../genometools/src/external/bzip2-1.0.6 \

            -I$(CURDIR)/../genometools/src/external/expat-2.0.1/lib \

            -I$(CURDIR)/../genometools/src/external/lua-5.1.5/src \

            -I$(CURDIR)/src -I$(CURDIR)/obj \

# these variables are exported by the configuration script

CC:=gcc

endif

# ...while those starting with GTH_ are for internal purposes only

GTH_CFLAGS:=-g -Wall -Wunused-parameter -pipe $(FPIC) -Wpointer-arith -fno-stack-protector -Wno-error=misleading-indentation

GTH_CFLAGS:=-g -Wall -Wunused-parameter -pipe $(FPIC) -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas

# mkvtree needs -DWITHLCP

# rnv needs -DUNISTD_H="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION="\"1.7.8\""

EXT_FLAGS:= -DWITHLCP -DUNISTD_H="<unistd.h>" -DEXPAT_H="<expat.h>" \

  GTH_LDFLAGS+=-Wl,--wrap=memcpy

endif

ifneq ($(SYSTEM),Darwin)

ifneq ($(MACHINE),ARMv6_hf)

GTH_CFLAGS+=-Wno-error=misleading-indentation

endif

endif

# system specific stuff (concerning 64bit compilation)

ifeq ($(SYSTEM),Darwin)

  ifeq ($(64bit),yes)

  RNVMAIN_OBJ+=../genometools/obj/src/memcpy.o

endif

LIBGENOMETHREADER_DIRS:= src/libgenomethreader

LIBGENOMETHREADER_DIRS:= src/libgenomethreader src/gth

# the GenomeThreader library

LIBGENOMETHREADER_SRC:=$(foreach DIR,$(LIBGENOMETHREADER_DIRS),$(wildcard $(DIR)/*.c))

all: lib/libgenomethreader.a bin/gth bin/gthconsensus bin/gthbssmfileinfo \

     bin/gthbssmbuild bin/gthbssmprint bin/gthbssmrmsd bin/gthbssmtrain \

     bin/gthfilestat bin/gthsplit bin/gthunit bin/gthgetseq bin/align_dna \

     bin/rnv

     bin/gthfilestat bin/gthmkbssmfiles bin/gthsplit bin/gthunit \

     bin/gthgetseq bin/align_dna bin/rnv

lib/libgenomethreader.a: obj/gth_config.h $(LIBGENOMETHREADER_OBJ)

	@echo "[link $(@F)]"

                                lib/libgenomethreader.a \

                                $(GTHLIBS) ../genometools/lib/libgenometools.a))

$(eval $(call PROGRAM_template, bin/gthmkbssmfiles, obj/src/gthmkbssmfiles.o \

                                lib/libgenomethreader.a \

                                $(GTHLIBS) ../genometools/lib/libgenometools.a))

$(eval $(call PROGRAM_template, bin/gthsplit, obj/src/gthsplit.o \

                                lib/libgenomethreader.a \

                                $(GTHLIBS) ../genometools/lib/libgenometools.a))

obj/old_train: ../genometools/bin/gt

	@echo "[write old BSSMs]"

	@../genometools/bin/gt dev gthmkbssmfiles bin/bssm

	@bin/gthmkbssmfiles bin/bssm

	@touch $@

obj/gthdata:

1.7.1

1.7.2

          speciestable.ispell

all: ispellall\

     gthmanual.pdf\

     gthlicense.pdf

     gthmanual.pdf

${GTHMANUALTMP}.tex: gthmanual.tex execcommand.pl

	#findemptyoutfiles.sh

\documentclass[12pt]{article}

\usepackage{times,url,a4wide,xspace}

\parindent0pt

\parskip5pt

\newcommand{\Software}[0]{\emph{GenomeThreader}\xspace}

\newcommand{\Licensorname}[0]{\emph{Gordon Gremme, Universit\"at Hamburg}\xspace}

\newcommand{\Thepaper}[0]{web-site: \par\url{http://www.genomethreader.org}\xspace}

\newcommand{\Email}[0]{\texttt{\small gordon@gremme.org}\xspace}

\newcommand{\Persontocontact}[0]{Gordon Gremme\xspace}

\newcommand{\Noncommercial}[0]{\\{\normalsize for non-commerical users}}

\newcommand{\Licensor}[0]{\textsc{Licensor}\xspace}

\newcommand{\Licensee}[0]{\textsc{Licensee}\xspace}

\newcommand{\Agreement}[0]{\textsc{Agreement}\xspace}

\newcommand{\Sites}[0]{\textsc{Sites}\xspace}

\newcommand{\Fillline}[0]{\rule{10cm}{1pt}}

\newcommand{\Paragraph}[2]{\item \textbf{#1:} #2}

\title{\Software License Agreement\Noncommercial}

\author{\vspace*{-1cm}}

\date{\vspace*{-1cm}\today}

\begin{document}

\maketitle

This document is the license agreement for the \Software Software Package.

There is no distribution fee for \Software for non commercial research

institutions. Commercial research institutions who want to use \Software

should directly contact \Persontocontact via Email at

\begin{center}

\Email

\end{center}

\Licensorname (\Licensor), as sole holder of all the proprietary rights to 

\Software grants to the licensee as defined in paragraph \ref{DefSites}

(\Licensee) a perpetual, non-exclusive, non-assignable, personal 

license to use the proprietary \Software software, subject to 

the conditions set forth below.

\begin{enumerate}

\Paragraph{Restricted License}{Use of \Software, or any part 

thereof, or any software derived in whole or in part therefrom, is 

restricted to use by \Licensee only, and is limited to the following 

uses unless \Licensor agrees otherwise by prior written agreement.

}

\begin{itemize}

\item

\Licensee is authorized to use \Software on all computers 

at the separate geographic locations itemized in paragraph \ref{DefSites} below 

(the \Sites) and at no other locations. The \Sites must include all 

locations from which remote (telephone or network) access will be 

made.

\item

\Licensee may not copy \Software, or any part thereof in 

any form, except for backup or archiving purposes, and for the 

purpose of distributing it to computers at the given \Sites. \Licensee 

agrees not to remove or destroy any proprietary markings or 

confidential legends placed upon or contained within \Software 

and any related materials.

\item

\Licensee may not sell, rent, sublicense, or otherwise distribute 

in any manner whatsoever \Software, or any part thereof, or 

any software derived in whole or in part therefrom, without the prior 

written approval of \Licensor.

\end{itemize}

\Paragraph{Title}{The \Agreement grants \Licensee no title or right of 

ownership in \Software, and no property rights in any 

copyrighted materials delivered hereunder.

}

\Paragraph{Non-Disclosure}{\Licensee agrees to receive and keep 

\Software in confidence and not to disclose it to any third 

party without the express written consent of \Licensor.

}

\Paragraph{Proper Credit and Recognition}{Appropriate credits consist 

of including in any documentation and publications about research 

using \Software a reference to the following \Thepaper

}

\Paragraph{Disclaimer of Warranty}{\Licensor provides \Software 

on an \textbf{as is} basis. \Licensor does not warrant its validity of 

performance, efficiency, or suitability, nor does \Licensor warrant 

that \Software is free from errors. All warranties, 

including without limitation, any warranty or merchantability or 

fitness for a particular purpose, are hereby excluded.

}

\Paragraph{Lack of Maintenance Services}{\Licensee understands and 

agrees that \Licensor (or any other person or entity with proprietary 

rights in the software licensed hereunder) is under no obligation to 

provide either maintenance services, update services, notices of 

latent defects, or correction of defects for \Software. 

\Licensor nevertheless reserves the right to update, modify, or 

discontinue this software at any time.

}

\Paragraph{Limitation of Liability, Indemnification}{Even if advised 

of the possibility of such damages, under no circumstances shall 

\Licensor (or any other person or entity with proprietary rights in 

the software licensed hereunder) be liable to \Licensee or any third 

party for direct, indirect, or consequential damages of any 

character, including, without limitation, loss of profits, loss of 

use, loss of good will, or computer failure or malfunction, 

regardless of the nature of the claim or action, whether in 

negligence or other tort, breach of contract, product liability, or 

otherwise. \Licensee agrees to indemnify \Licensor (or any other person 

or entity with proprietary rights in the software licensed hereunder) 

for any and all liability it may incur to third parties resulting 

from \Licensee's use of 

\Software.

%\Software, subject to the limits of Florida law.

}

\Paragraph{Applicable Law}{This \Agreement is deemed to be made under, 

and shall be governed by the laws of the Federal Republic of Germany. 

Both parties consent to jurisdiction in the Federal Republic of Germany.

German law applies to this \Agreement without giving effect to its 

conflict of laws (IPR) provisions. 

}

\Paragraph{Binding Effect Agreement}{This \Agreement shall be binding 

upon and inure to the benefit of the heirs, successors and assigns of 

\Licensee, but \Licensee may not assign this \Agreement or any of its 

rights or obligations hereunder without the prior written approval of 

\Licensor.

}

\Paragraph{Entire Agreement}{This \Agreement represents the complete 

and exclusive statement of the agreements between the parties 

relating to the licensing of \Software, and supersedes all 

prior and simultaneous agreements and representations between them 

relating to such licensing. This \Agreement may not be modified except 

with the written approval of the \Licensor.

}

\newpage

\Paragraph{Definition of Sites}{

The separate geographical locations 

referred to as \Sites are listed below:

\begin{center}

\begin{tabular}{ll}

1.&\Fillline\\[5mm]

2.&\Fillline\\[5mm]

3.&\Fillline

\end{tabular}

\end{center}

}

\label{DefSites}

\Paragraph{Mailing Address}{A signed copy of this license \Agreement

shall be mailed or sent as a FAX by \Licensee to \Licensor at the 

following address:

\begin{tabular}{@{}l}

\Persontocontact\\

Zentrum f\"ur Bioinformatik\\

Universit\"at Hamburg\\

Bundesstrasse 43\\

20146 Hamburg\\

Germany\\

FAX: +49 40 42838 7312

\end{tabular}

An Email describing how to download \Software shall be send by \Licensor to 

\Licensee to the following Email address:

\begin{center}

\begin{tabular}{lc}

Electronic Mail:&\Fillline\\[5mm]

Name:&\Fillline

\end{tabular}

\end{center}

In previous cases, we had problems with our FAX machine or could not

decipher the E-mail address of the \Licensor.

To verify that we have received the FAX properly, you may want send a 

short E-mail to \Email stating that you have send the FAX. 

Once we have received the signed agreement we will process it a soon as 

possible. 

}

\Paragraph{Execution and Delivery}{By its execution and delivery of 

this \Agreement, \Licensee covenants and agrees to be bound by the 

above stated terms and conditions, and warrants and represents that 

the person or persons signing this Licensing \Agreement is authorized 

to bind and commit \Licensee to this \Agreement.

}

\end{enumerate}

\begin{center}

\begin{tabular}{lc}

Research Institution:&\Fillline\\[5mm]

Address:&\Fillline\\[5mm]

Signature:&\Fillline\\[5mm]

Name and Title:&\Fillline\\[5mm]

Date:&\Fillline

\end{tabular}

\end{center}

\end{document}

This directory contains the binary distribution of GenomeThreader (gth).

All rights reserved. Do not distribute.

It contains the following directories