--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/AUTHORS	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,2 @@
+See README file.
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/COPYING	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,340 @@
+		    GNU GENERAL PUBLIC LICENSE
+		       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+			    Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
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+
+  Finally, any free program is threatened constantly by software
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+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+		    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License.  The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language.  (Hereinafter, translation is included without limitation in
+the term "modification".)  Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope.  The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+  1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+  2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+    a) You must cause the modified files to carry prominent notices
+    stating that you changed the files and the date of any change.
+
+    b) You must cause any work that you distribute or publish, that in
+    whole or in part contains or is derived from the Program or any
+    part thereof, to be licensed as a whole at no charge to all third
+    parties under the terms of this License.
+
+    c) If the modified program normally reads commands interactively
+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
+    announcement including an appropriate copyright notice and a
+    notice that there is no warranty (or else, saying that you provide
+    a warranty) and that users may redistribute the program under
+    these conditions, and telling the user how to view a copy of this
+    License.  (Exception: if the Program itself is interactive but
+    does not normally print such an announcement, your work based on
+    the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole.  If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works.  But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+    a) Accompany it with the complete corresponding machine-readable
+    source code, which must be distributed under the terms of Sections
+    1 and 2 above on a medium customarily used for software interchange; or,
+
+    b) Accompany it with a written offer, valid for at least three
+    years, to give any third party, for a charge no more than your
+    cost of physically performing source distribution, a complete
+    machine-readable copy of the corresponding source code, to be
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+    customarily used for software interchange; or,
+
+    c) Accompany it with the information you received as to the offer
+    to distribute corresponding source code.  (This alternative is
+    allowed only for noncommercial distribution and only if you
+    received the program in object code or executable form with such
+    an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
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+If distribution of executable or object code is made by offering
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+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+  4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License.  Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+  5. You are not required to accept this License, since you have not
+signed it.  However, nothing else grants you permission to modify or
+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+  6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+			    NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+		     END OF TERMS AND CONDITIONS
+
+	    How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program 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
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program; if not, write to the Free Software
+    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year  name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Library General
+Public License instead of this License.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/ChangeLog	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,17 @@
+Version 0.0.1 11-Mar-2012
+        Beta version.
+Version 0.0.1 09-Jun-2012
+        Update, 5 methods added. Some method names changed.
+Version 0.0.1 26-Sep-2012
+	Update, 1 method added.
+Version 1.0.1 07-Jul-2013
+	Map method conversion.
+	Document re-enforecment.
+	RESTification
+	EDAM ontology mapping
+Version 1.0.2 28-Oct-2013
+	Update EMBOSS-6.6.0
+Version 1.0.3 09-Feb-2015
+	Refactoring
+	Finish RESTification
+	Implement "-tai" option in "gcai"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/INSTALL	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,370 @@
+Installation Instructions
+*************************
+
+Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
+Inc.
+
+   Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved.  This file is offered as-is,
+without warranty of any kind.
+
+Basic Installation
+==================
+
+   Briefly, the shell command `./configure && make && make install'
+should configure, build, and install this package.  The following
+more-detailed instructions are generic; see the `README' file for
+instructions specific to this package.  Some packages provide this
+`INSTALL' file but do not implement all of the features documented
+below.  The lack of an optional feature in a given package is not
+necessarily a bug.  More recommendations for GNU packages can be found
+in *note Makefile Conventions: (standards)Makefile Conventions.
+
+   The `configure' shell script attempts to guess correct values for
+various system-dependent variables used during compilation.  It uses
+those values to create a `Makefile' in each directory of the package.
+It may also create one or more `.h' files containing system-dependent
+definitions.  Finally, it creates a shell script `config.status' that
+you can run in the future to recreate the current configuration, and a
+file `config.log' containing compiler output (useful mainly for
+debugging `configure').
+
+   It can also use an optional file (typically called `config.cache'
+and enabled with `--cache-file=config.cache' or simply `-C') that saves
+the results of its tests to speed up reconfiguring.  Caching is
+disabled by default to prevent problems with accidental use of stale
+cache files.
+
+   If you need to do unusual things to compile the package, please try
+to figure out how `configure' could check whether to do them, and mail
+diffs or instructions to the address given in the `README' so they can
+be considered for the next release.  If you are using the cache, and at
+some point `config.cache' contains results you don't want to keep, you
+may remove or edit it.
+
+   The file `configure.ac' (or `configure.in') is used to create
+`configure' by a program called `autoconf'.  You need `configure.ac' if
+you want to change it or regenerate `configure' using a newer version
+of `autoconf'.
+
+   The simplest way to compile this package is:
+
+  1. `cd' to the directory containing the package's source code and type
+     `./configure' to configure the package for your system.
+
+     Running `configure' might take a while.  While running, it prints
+     some messages telling which features it is checking for.
+
+  2. Type `make' to compile the package.
+
+  3. Optionally, type `make check' to run any self-tests that come with
+     the package, generally using the just-built uninstalled binaries.
+
+  4. Type `make install' to install the programs and any data files and
+     documentation.  When installing into a prefix owned by root, it is
+     recommended that the package be configured and built as a regular
+     user, and only the `make install' phase executed with root
+     privileges.
+
+  5. Optionally, type `make installcheck' to repeat any self-tests, but
+     this time using the binaries in their final installed location.
+     This target does not install anything.  Running this target as a
+     regular user, particularly if the prior `make install' required
+     root privileges, verifies that the installation completed
+     correctly.
+
+  6. You can remove the program binaries and object files from the
+     source code directory by typing `make clean'.  To also remove the
+     files that `configure' created (so you can compile the package for
+     a different kind of computer), type `make distclean'.  There is
+     also a `make maintainer-clean' target, but that is intended mainly
+     for the package's developers.  If you use it, you may have to get
+     all sorts of other programs in order to regenerate files that came
+     with the distribution.
+
+  7. Often, you can also type `make uninstall' to remove the installed
+     files again.  In practice, not all packages have tested that
+     uninstallation works correctly, even though it is required by the
+     GNU Coding Standards.
+
+  8. Some packages, particularly those that use Automake, provide `make
+     distcheck', which can by used by developers to test that all other
+     targets like `make install' and `make uninstall' work correctly.
+     This target is generally not run by end users.
+
+Compilers and Options
+=====================
+
+   Some systems require unusual options for compilation or linking that
+the `configure' script does not know about.  Run `./configure --help'
+for details on some of the pertinent environment variables.
+
+   You can give `configure' initial values for configuration parameters
+by setting variables in the command line or in the environment.  Here
+is an example:
+
+     ./configure CC=c99 CFLAGS=-g LIBS=-lposix
+
+   *Note Defining Variables::, for more details.
+
+Compiling For Multiple Architectures
+====================================
+
+   You can compile the package for more than one kind of computer at the
+same time, by placing the object files for each architecture in their
+own directory.  To do this, you can use GNU `make'.  `cd' to the
+directory where you want the object files and executables to go and run
+the `configure' script.  `configure' automatically checks for the
+source code in the directory that `configure' is in and in `..'.  This
+is known as a "VPATH" build.
+
+   With a non-GNU `make', it is safer to compile the package for one
+architecture at a time in the source code directory.  After you have
+installed the package for one architecture, use `make distclean' before
+reconfiguring for another architecture.
+
+   On MacOS X 10.5 and later systems, you can create libraries and
+executables that work on multiple system types--known as "fat" or
+"universal" binaries--by specifying multiple `-arch' options to the
+compiler but only a single `-arch' option to the preprocessor.  Like
+this:
+
+     ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+                 CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+                 CPP="gcc -E" CXXCPP="g++ -E"
+
+   This is not guaranteed to produce working output in all cases, you
+may have to build one architecture at a time and combine the results
+using the `lipo' tool if you have problems.
+
+Installation Names
+==================
+
+   By default, `make install' installs the package's commands under
+`/usr/local/bin', include files under `/usr/local/include', etc.  You
+can specify an installation prefix other than `/usr/local' by giving
+`configure' the option `--prefix=PREFIX', where PREFIX must be an
+absolute file name.
+
+   You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files.  If you
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses
+PREFIX as the prefix for installing programs and libraries.
+Documentation and other data files still use the regular prefix.
+
+   In addition, if you use an unusual directory layout you can give
+options like `--bindir=DIR' to specify different values for particular
+kinds of files.  Run `configure --help' for a list of the directories
+you can set and what kinds of files go in them.  In general, the
+default for these options is expressed in terms of `${prefix}', so that
+specifying just `--prefix' will affect all of the other directory
+specifications that were not explicitly provided.
+
+   The most portable way to affect installation locations is to pass the
+correct locations to `configure'; however, many packages provide one or
+both of the following shortcuts of passing variable assignments to the
+`make install' command line to change installation locations without
+having to reconfigure or recompile.
+
+   The first method involves providing an override variable for each
+affected directory.  For example, `make install
+prefix=/alternate/directory' will choose an alternate location for all
+directory configuration variables that were expressed in terms of
+`${prefix}'.  Any directories that were specified during `configure',
+but not in terms of `${prefix}', must each be overridden at install
+time for the entire installation to be relocated.  The approach of
+makefile variable overrides for each directory variable is required by
+the GNU Coding Standards, and ideally causes no recompilation.
+However, some platforms have known limitations with the semantics of
+shared libraries that end up requiring recompilation when using this
+method, particularly noticeable in packages that use GNU Libtool.
+
+   The second method involves providing the `DESTDIR' variable.  For
+example, `make install DESTDIR=/alternate/directory' will prepend
+`/alternate/directory' before all installation names.  The approach of
+`DESTDIR' overrides is not required by the GNU Coding Standards, and
+does not work on platforms that have drive letters.  On the other hand,
+it does better at avoiding recompilation issues, and works well even
+when some directory options were not specified in terms of `${prefix}'
+at `configure' time.
+
+Optional Features
+=================
+
+   If the package supports it, you can cause programs to be installed
+with an extra prefix or suffix on their names by giving `configure' the
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
+
+   Some packages pay attention to `--enable-FEATURE' options to
+`configure', where FEATURE indicates an optional part of the package.
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE
+is something like `gnu-as' or `x' (for the X Window System).  The
+`README' should mention any `--enable-' and `--with-' options that the
+package recognizes.
+
+   For packages that use the X Window System, `configure' can usually
+find the X include and library files automatically, but if it doesn't,
+you can use the `configure' options `--x-includes=DIR' and
+`--x-libraries=DIR' to specify their locations.
+
+   Some packages offer the ability to configure how verbose the
+execution of `make' will be.  For these packages, running `./configure
+--enable-silent-rules' sets the default to minimal output, which can be
+overridden with `make V=1'; while running `./configure
+--disable-silent-rules' sets the default to verbose, which can be
+overridden with `make V=0'.
+
+Particular systems
+==================
+
+   On HP-UX, the default C compiler is not ANSI C compatible.  If GNU
+CC is not installed, it is recommended to use the following options in
+order to use an ANSI C compiler:
+
+     ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
+
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+
+   HP-UX `make' updates targets which have the same time stamps as
+their prerequisites, which makes it generally unusable when shipped
+generated files such as `configure' are involved.  Use GNU `make'
+instead.
+
+   On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
+parse its `<wchar.h>' header file.  The option `-nodtk' can be used as
+a workaround.  If GNU CC is not installed, it is therefore recommended
+to try
+
+     ./configure CC="cc"
+
+and if that doesn't work, try
+
+     ./configure CC="cc -nodtk"
+
+   On Solaris, don't put `/usr/ucb' early in your `PATH'.  This
+directory contains several dysfunctional programs; working variants of
+these programs are available in `/usr/bin'.  So, if you need `/usr/ucb'
+in your `PATH', put it _after_ `/usr/bin'.
+
+   On Haiku, software installed for all users goes in `/boot/common',
+not `/usr/local'.  It is recommended to use the following options:
+
+     ./configure --prefix=/boot/common
+
+Specifying the System Type
+==========================
+
+   There may be some features `configure' cannot figure out
+automatically, but needs to determine by the type of machine the package
+will run on.  Usually, assuming the package is built to be run on the
+_same_ architectures, `configure' can figure that out, but if it prints
+a message saying it cannot guess the machine type, give it the
+`--build=TYPE' option.  TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name which has the form:
+
+     CPU-COMPANY-SYSTEM
+
+where SYSTEM can have one of these forms:
+
+     OS
+     KERNEL-OS
+
+   See the file `config.sub' for the possible values of each field.  If
+`config.sub' isn't included in this package, then this package doesn't
+need to know the machine type.
+
+   If you are _building_ compiler tools for cross-compiling, you should
+use the option `--target=TYPE' to select the type of system they will
+produce code for.
+
+   If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with `--host=TYPE'.
+
+Sharing Defaults
+================
+
+   If you want to set default values for `configure' scripts to share,
+you can create a site shell script called `config.site' that gives
+default values for variables like `CC', `cache_file', and `prefix'.
+`configure' looks for `PREFIX/share/config.site' if it exists, then
+`PREFIX/etc/config.site' if it exists.  Or, you can set the
+`CONFIG_SITE' environment variable to the location of the site script.
+A warning: not all `configure' scripts look for a site script.
+
+Defining Variables
+==================
+
+   Variables not defined in a site shell script can be set in the
+environment passed to `configure'.  However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost.  In order to avoid this problem, you should set
+them in the `configure' command line, using `VAR=value'.  For example:
+
+     ./configure CC=/usr/local2/bin/gcc
+
+causes the specified `gcc' to be used as the C compiler (unless it is
+overridden in the site shell script).
+
+Unfortunately, this technique does not work for `CONFIG_SHELL' due to
+an Autoconf limitation.  Until the limitation is lifted, you can use
+this workaround:
+
+     CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
+
+`configure' Invocation
+======================
+
+   `configure' recognizes the following options to control how it
+operates.
+
+`--help'
+`-h'
+     Print a summary of all of the options to `configure', and exit.
+
+`--help=short'
+`--help=recursive'
+     Print a summary of the options unique to this package's
+     `configure', and exit.  The `short' variant lists options used
+     only in the top level, while the `recursive' variant lists options
+     also present in any nested packages.
+
+`--version'
+`-V'
+     Print the version of Autoconf used to generate the `configure'
+     script, and exit.
+
+`--cache-file=FILE'
+     Enable the cache: use and save the results of the tests in FILE,
+     traditionally `config.cache'.  FILE defaults to `/dev/null' to
+     disable caching.
+
+`--config-cache'
+`-C'
+     Alias for `--cache-file=config.cache'.
+
+`--quiet'
+`--silent'
+`-q'
+     Do not print messages saying which checks are being made.  To
+     suppress all normal output, redirect it to `/dev/null' (any error
+     messages will still be shown).
+
+`--srcdir=DIR'
+     Look for the package's source code in directory DIR.  Usually
+     `configure' can determine that directory automatically.
+
+`--prefix=DIR'
+     Use DIR as the installation prefix.  *note Installation Names::
+     for more details, including other options available for fine-tuning
+     the installation locations.
+
+`--no-create'
+`-n'
+     Run the configure checks, but stop before creating any output
+     files.
+
+`configure' also accepts some other, not widely useful, options.  Run
+`configure --help' for more details.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/Makefile.am	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,13 @@
+#
+
+SUBDIRS = src acd doc
+
+EXTRA_DIST = gsoap depcomp ltmain.sh config.sub config.guess data
+
+# tar to pick up the other directories
+# then remove any CVS subdirectories
+
+dist-hook:
+	tar cBf - acd | ( cd $(distdir); tar xBf - ; cd acd; rm -rf CVS ) 
+	tar cBf - doc | ( cd $(distdir); tar xBf - ; cd doc; rm -rf CVS; rm -rf master) 
+	tar cBf - include | ( cd $(distdir); tar xBf - ; cd include; rm -rf CVS ) 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/NEWS	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,1 @@
+11/3/2012      See Changelog

--- /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.
+
+*****************************************************************************/