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README
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/* GEMBASSY ver 1.0.3 *********************************************************
All rights reserved. Copyright (C) 2012-2013 by ITAYA Kotone.
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.
*****************************************************************************/