--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/README	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,223 @@
+
+/* 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.
+
+*****************************************************************************/