--- a/GEMBASSY-1.0.3/README	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,223 +0,0 @@
-
-/* GEMBASSY ver 1.0.3 *********************************************************
-
-  All rights reserved. Copyright (C) 2012-2013 by ITAYA Hidetoshi.
-
-  This EMBASSY package is free software. You can redistribute it and/or modify
-  it under the terms of the GNU General Public License as published by the
-  Free Software Foundation, either version 2 of the License, or any later
-  version.
-
-  See also GNU General Public License Version 2, included in this
-  package as COPYING.
-
-*****************************************************************************/
-
-
-
-/* About *********************************************************************
-
-  This is an EMBASSY package for the utilization of G-language SOAP service.
-
-  All of the tools included in this package are wrapper programs to
-  utilize G-language SOAP service, which are web APIs to access the methods
-  of G-language Genome Analysis Environment (G-language GAE); a powerful
-  workbench for genome analysis.
-
-  Detailed documentation on G-language GAE methods are availabe at:
-  http://www.g-language.org/wiki/soap
-
-  The EMBOSS Explorer interface is available at:
-  http://soap.g-language.org/gembassy/emboss_explorer
-
-*****************************************************************************/
-
-
-
-/* Installation **************************************************************
-
-REQUIREMENTS
-   EMBOSS (> 6.6.0) - This EMBASSY package requires EMBOSS version 6.6.0 or
-                      above.
-   libcurl-devel (> 7.29.0) - Required for file POST
-
-   A UNIX-like operating system
-
-INSTALLATION
-  Is EMBOSS already installed in your system?
-    Yes: Go to "EMBOSS is already installed" section.
-    No: Go to "Install from EMBOSS" section.
-
-  Install from EMBOSS:
-  Root users
-    In the following examples we assume the downloaded EMBOSS archive filename
-    is emboss-latest.tar.gz
-
-    1. Download and compile EMBOSS source code
-      % wget ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz
-      (or "curl -O ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz")
-      % tar zxf emboss-latest.tar.gz
-      % cd EMBOSS-6.6.0
-      % ./configure
-      % make
-      % sudo make install
-
-    2. Make "embassy" directory in the EMBOSS-6.6.0/ directory if it does not
-       exist and go into the directory.
-      % mkdir embassy
-      % cd embassy
-
-    3. Download and compile the GEMBASSY source code
-      % wget http://soap.g-language.org/gembassy/source/GEMBASSSY-1.0.3.tar.gz
-      (or "curl -O http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz")
-      % tar zxvf GEMBASSY-1.0.3.tar.gz
-      % cd GEMBASSY-1.0.3
-      ( EMBOSS-6.6.0/embassy/GEMBASSY-1.0.3 )
-      % ./configure
-      % make
-      % sudo make install
-
-  Non-root users
-    When running the './configure' command do the following instead:
-      % ./configure --prefix=/PATH/TO/DIR/ (ex. --prefix=$HOME/opt)
-
-  EMBOSS is already installed:
-    When EMBOSS is already installed, GEMBASSY must be installed to the exact
-    same directory as the existing EMBOSS.
-
-    If non-root users wish to install GEMBASSY separately, first install the
-    EMBOSS package on top of the home directory.
-
-    The following commands assume you have EMBOSS installed in the
-    /PATH/TO/EMBOSS/ directory.
-      % wget http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz
-      (or "curl -O http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz")
-      % tar zxf GEMBASSY-1.0.3.tar.gz
-      % cd GEMBASSY-1.0.3
-      % ./configure --prefix=/PATH/TO/EMBOSS/ (ex. --prefix=/usr/local)
-      % make
-      % make install
-
-
-    Installing custom EMBOSS configuration files
-      We highly recommend users to install the custom EMBOSS configuration files
-      from the KBWS package. The configuration file provides database definition
-      for various databases, allowing versatile access to various sequence
-      entries.
-
-      % wget http://soap.g-language.org/kbws/embossrc
-       (or "curl -O http://soap.g-language.org/kbws/embossrc")
-      % mv embossrc ~/.embossrc
-
-    Then rewrite the "emboss_acdroot" and "emboss_data" value in ~/.embossrc
-    file to the corresponding directories.
-    (ex. emboss_acdroot = ~/opt/share/EMBOSS/acd)
-    (ex. emboss_data = ~/opt/share/EMBOSS/data)
-
-  Update of EMBOSS
-    When users are upgrading EMBOSS, please be sure to uninstall old versions
-    of EMBOSS and GEMBASSY. If you override them, some older versions of files
-    may cause errors.
-
-  NOTE - automake problem
-    If the source code is cloned from the GitHub Repository, there are
-    known problems with automake version mismatches which stop the compilation
-    of the source. Follow the steps below in (NOTE - libtool problem) to
-    solve this problem.
-
-  NOTE - libtool problem
-    On some systems there may be compatibility problems with different
-    automake, autoconf or libtool versions. If a libtool problem
-    arises you can try deleting the following files if they exist:
-
-      config.cache
-      ltmain.sh
-      ltconfig
-      libtool
-
-    and then type
-      % aclocal -I m4
-      % autoconf
-      % automake -a
-
-    and then retry make.
-
-    If you have 'autoreconf' in your system
-      % autoreconf -fi
-
-    will do the trick.
-
-*****************************************************************************/
-
-
-
-/* QuickStart ****************************************************************
-
-DATABASE DEFINITION
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-   Input files used in the examples are provided in the data/ directory.
-
-   INSTALLATION:
-     % wget http://soap.g-language.org/kbws/embossrc
-      (or "curl -O http://soap.g-language.org/kbws/embossrc")
-     % mv embossrc ~/.embossrc
-
-    Then rewrite the "emboss_acdroot" and "emboss_data" value in ~/.embossrc
-    file to the corresponding directories.
-    (ex. emboss_acdroot = ~/share/EMBOSS/acd)
-    (ex. emboss_data = ~/share/EMBOSS/data)
-
-INFORMATION OF GEMBASSY TOOLS
-   List of all tools
-      For a list of all tools included in GEMBASSY use
-      % wossname -showembassy GEMBASSY
-
-   Documentation
-      Detailed documentation are available to be viewed with the "tfm"
-      utility included in EMBOSS.
-      Here is an example for "gaminoinfo"
-      % tfm gaminoinfo
-
-USAGE EXAMPLE
-   The following examples show basic usages of three GEMBASSY tools and the
-   different ways of passing input. Example 1. uses database definition, 2.
-   uses the accid option, and 3. uses the sequence accession ID as input.
-   1. ggcskew (GC skew)
-      % ggcskew -plot -graph cps refseqn:NC_000913
-      Calculates the GC skew of the input sequence
-      Created ggcskew.ps
-
-   2. ggcsi (GC Skew Index)
-      % ggcsi accid.fasta -accid stdout
-      GC Skew Index: an index for strand-specefic mutational bias
-      Input nucleotide sequence: refseqn:NC_000964
-      Sequence: NC_000964 GCSI: 0.214855185905019 SA: 976.152832384745 DIST: 170.245783
-
-   3. greporiter (Replication Origin and Terminus)
-      % greporiter -outfile stdout
-      Get the positions of replication origin and terminus
-      Input nucleotide sequence: accid.fasta
-      Sequence: NC_000913 Origin: 3923881 Terminus: 1550412
-
-*****************************************************************************/
-
-
-
-/* Content *******************************************************************
-
-gSOAP Toolkit
-   This EMBASSY package is dependant on gSOAP Toolkit for SOAP transfer,
-   included in the gsoap/ directory. It is used automatically during
-   compilation.
-
-*****************************************************************************/
-
-
-
-/* Contact *******************************************************************
-
-Hidetoshi Itaya (celery @ g-language.org)
-   Institute for Advanced Biosciences, Keio University.
-
-*****************************************************************************/