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1
2 /* GEMBASSY ver 1.0.3 *********************************************************
3
4 All rights reserved. Copyright (C) 2012-2013 by ITAYA Hidetoshi.
5
6 This EMBASSY package is free software. You can redistribute it and/or modify
7 it under the terms of the GNU General Public License as published by the
8 Free Software Foundation, either version 2 of the License, or any later
9 version.
10
11 See also GNU General Public License Version 2, included in this
12 package as COPYING.
13
14 *****************************************************************************/
15
16
17
18 /* About *********************************************************************
19
20 This is an EMBASSY package for the utilization of G-language SOAP service.
21
22 All of the tools included in this package are wrapper programs to
23 utilize G-language SOAP service, which are web APIs to access the methods
24 of G-language Genome Analysis Environment (G-language GAE); a powerful
25 workbench for genome analysis.
26
27 Detailed documentation on G-language GAE methods are availabe at:
28 http://www.g-language.org/wiki/soap
29
30 The EMBOSS Explorer interface is available at:
31 http://soap.g-language.org/gembassy/emboss_explorer
32
33 *****************************************************************************/
34
35
36
37 /* Installation **************************************************************
38
39 REQUIREMENTS
40 EMBOSS (> 6.6.0) - This EMBASSY package requires EMBOSS version 6.6.0 or
41 above.
42 libcurl-devel (> 7.29.0) - Required for file POST
43
44 A UNIX-like operating system
45
46 INSTALLATION
47 Is EMBOSS already installed in your system?
48 Yes: Go to "EMBOSS is already installed" section.
49 No: Go to "Install from EMBOSS" section.
50
51 Install from EMBOSS:
52 Root users
53 In the following examples we assume the downloaded EMBOSS archive filename
54 is emboss-latest.tar.gz
55
56 1. Download and compile EMBOSS source code
57 % wget ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz
58 (or "curl -O ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz")
59 % tar zxf emboss-latest.tar.gz
60 % cd EMBOSS-6.6.0
61 % ./configure
62 % make
63 % sudo make install
64
65 2. Make "embassy" directory in the EMBOSS-6.6.0/ directory if it does not
66 exist and go into the directory.
67 % mkdir embassy
68 % cd embassy
69
70 3. Download and compile the GEMBASSY source code
71 % wget http://soap.g-language.org/gembassy/source/GEMBASSSY-1.0.3.tar.gz
72 (or "curl -O http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz")
73 % tar zxvf GEMBASSY-1.0.3.tar.gz
74 % cd GEMBASSY-1.0.3
75 ( EMBOSS-6.6.0/embassy/GEMBASSY-1.0.3 )
76 % ./configure
77 % make
78 % sudo make install
79
80 Non-root users
81 When running the './configure' command do the following instead:
82 % ./configure --prefix=/PATH/TO/DIR/ (ex. --prefix=$HOME/opt)
83
84 EMBOSS is already installed:
85 When EMBOSS is already installed, GEMBASSY must be installed to the exact
86 same directory as the existing EMBOSS.
87
88 If non-root users wish to install GEMBASSY separately, first install the
89 EMBOSS package on top of the home directory.
90
91 The following commands assume you have EMBOSS installed in the
92 /PATH/TO/EMBOSS/ directory.
93 % wget http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz
94 (or "curl -O http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz")
95 % tar zxf GEMBASSY-1.0.3.tar.gz
96 % cd GEMBASSY-1.0.3
97 % ./configure --prefix=/PATH/TO/EMBOSS/ (ex. --prefix=/usr/local)
98 % make
99 % make install
100
101
102 Installing custom EMBOSS configuration files
103 We highly recommend users to install the custom EMBOSS configuration files
104 from the KBWS package. The configuration file provides database definition
105 for various databases, allowing versatile access to various sequence
106 entries.
107
108 % wget http://soap.g-language.org/kbws/embossrc
109 (or "curl -O http://soap.g-language.org/kbws/embossrc")
110 % mv embossrc ~/.embossrc
111
112 Then rewrite the "emboss_acdroot" and "emboss_data" value in ~/.embossrc
113 file to the corresponding directories.
114 (ex. emboss_acdroot = ~/opt/share/EMBOSS/acd)
115 (ex. emboss_data = ~/opt/share/EMBOSS/data)
116
117 Update of EMBOSS
118 When users are upgrading EMBOSS, please be sure to uninstall old versions
119 of EMBOSS and GEMBASSY. If you override them, some older versions of files
120 may cause errors.
121
122 NOTE - automake problem
123 If the source code is cloned from the GitHub Repository, there are
124 known problems with automake version mismatches which stop the compilation
125 of the source. Follow the steps below in (NOTE - libtool problem) to
126 solve this problem.
127
128 NOTE - libtool problem
129 On some systems there may be compatibility problems with different
130 automake, autoconf or libtool versions. If a libtool problem
131 arises you can try deleting the following files if they exist:
132
133 config.cache
134 ltmain.sh
135 ltconfig
136 libtool
137
138 and then type
139 % aclocal -I m4
140 % autoconf
141 % automake -a
142
143 and then retry make.
144
145 If you have 'autoreconf' in your system
146 % autoreconf -fi
147
148 will do the trick.
149
150 *****************************************************************************/
151
152
153
154 /* QuickStart ****************************************************************
155
156 DATABASE DEFINITION
157 The database definitions for following commands are available at
158 http://soap.g-language.org/kbws/embossrc
159 Input files used in the examples are provided in the data/ directory.
160
161 INSTALLATION:
162 % wget http://soap.g-language.org/kbws/embossrc
163 (or "curl -O http://soap.g-language.org/kbws/embossrc")
164 % mv embossrc ~/.embossrc
165
166 Then rewrite the "emboss_acdroot" and "emboss_data" value in ~/.embossrc
167 file to the corresponding directories.
168 (ex. emboss_acdroot = ~/share/EMBOSS/acd)
169 (ex. emboss_data = ~/share/EMBOSS/data)
170
171 INFORMATION OF GEMBASSY TOOLS
172 List of all tools
173 For a list of all tools included in GEMBASSY use
174 % wossname -showembassy GEMBASSY
175
176 Documentation
177 Detailed documentation are available to be viewed with the "tfm"
178 utility included in EMBOSS.
179 Here is an example for "gaminoinfo"
180 % tfm gaminoinfo
181
182 USAGE EXAMPLE
183 The following examples show basic usages of three GEMBASSY tools and the
184 different ways of passing input. Example 1. uses database definition, 2.
185 uses the accid option, and 3. uses the sequence accession ID as input.
186 1. ggcskew (GC skew)
187 % ggcskew -plot -graph cps refseqn:NC_000913
188 Calculates the GC skew of the input sequence
189 Created ggcskew.ps
190
191 2. ggcsi (GC Skew Index)
192 % ggcsi accid.fasta -accid stdout
193 GC Skew Index: an index for strand-specefic mutational bias
194 Input nucleotide sequence: refseqn:NC_000964
195 Sequence: NC_000964 GCSI: 0.214855185905019 SA: 976.152832384745 DIST: 170.245783
196
197 3. greporiter (Replication Origin and Terminus)
198 % greporiter -outfile stdout
199 Get the positions of replication origin and terminus
200 Input nucleotide sequence: accid.fasta
201 Sequence: NC_000913 Origin: 3923881 Terminus: 1550412
202
203 *****************************************************************************/
204
205
206
207 /* Content *******************************************************************
208
209 gSOAP Toolkit
210 This EMBASSY package is dependant on gSOAP Toolkit for SOAP transfer,
211 included in the gsoap/ directory. It is used automatically during
212 compilation.
213
214 *****************************************************************************/
215
216
217
218 /* Contact *******************************************************************
219
220 Hidetoshi Itaya (celery @ g-language.org)
221 Institute for Advanced Biosciences, Keio University.
222
223 *****************************************************************************/