/* GEMBASSY ver 1.0.1 *********************************************************

  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 (> 6.5.7) - This EMBASSY package requires EMBOSS version 6.5.7 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-6.5.7
      % ./configure
      % make
      % sudo make install

    2. Make "embassy" directory in the EMBOSS-6.5.7/ 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-1.0.1.tar.gz
      (or "curl -O http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.1.tar.gz")
      % tar zxf GEMBASSY-1.0.1.tar.gz
      % cd GEMBASSY-1.0.1
      ( EMBOSS-6.5.7/embassy/GEMBASSY-1.0.1 )
      % ./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-1.0.1.tar.gz
      (or "curl -O http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.1.tar.gz")
      % tar zxf GEMBASSY-1.0.1.tar.gz
      % cd GEMBASSY-1.0.1
      % ./configure --prefix=/PATH/TO/EMBOSS/ (ex. --prefix=/usr/local)
      % make
      % make install


    Installing custom EMBOSS configuration files
      We highly reccomend users installing 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 = ~/share/EMBOSS/acd)
    (ex. emboss_data = ~/share/EMBOSS/data)

  Update of EMBOSS
    When users are upgrading EMBOSS, please be sure to uninstall old version
    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.

*****************************************************************************/