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  <TITLE>
  EMBOSS: jembossctl
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<a href="index.html" onmouseover="self.status='Go to the EMBOSS home page';return true">
<img border=0 src="emboss_icon.gif" alt="" width=55 height=55>
</a>
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<H2>
EMBOSS: jembossctl
</H2>
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<H1>
Program jembossctl
</H1>
<H2>
    Function
</H2>
Jemboss Authentication Control

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DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
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<H2>
    Description
</H2>

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        This is what the user looks at to find out if this program will do what he wants. 
        Long description.
        Why it is useful.
        When it should/shouldn't be used.
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<b>jembossctl</b> should not be run by typical users.  It is a slave
program for the Jemboss server.  If this means nothing to you, then you
do not need to know anything more, just ignore this program. 

<p>

If you are setting up a Jemboss server (This is not the Jemboss
interface that anyone can download, it is the software that listens to
the Jemboss interfaces and runs the EMBOSS programs for you), then this
program should be 'chmod 4755' to get root.  Details are to be found on
the Jemboss web pages. 










<H2>
    Usage
</H2>

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	Example usage, as run from the command-line.
        Many examples illustrating different behaviours is good.
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It is not used by normal users. It is only ever run by other programs.











<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
   Mandatory qualifiers:
  [-sock]              string     Pipe file

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#f5f5ff">
<tr bgcolor="#FFFFD0">
<th align="left" colspan=2>Mandatory qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>[-sock]<br>(Parameter 1)</td>
<td>Pipe file</td>
<td>Any string is accepted</td>
<td>/tmp/emboss</td>
</tr>

<tr bgcolor="#FFFFD0">
<th align="left" colspan=2>Optional qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td colspan=4>(none)</td>
</tr>

<tr bgcolor="#FFFFD0">
<th align="left" colspan=2>Advanced qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td colspan=4>(none)</td>
</tr>

</table>


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DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
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<H2>
    Input file format
</H2>

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        This includes example input file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null input, etc. 
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Not applicable.












<H2>
    Output file format
</H2>

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        This includes example output file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null output, errors etc. 
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Not applicable.

















<H2>
    Data files
</H2>

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        Any data files used (e.g. translation table file)
        This includes example data file formats if they are
        not obvious.
	If you wish to include the standard description of what data
	files are and how to use embossdata to inspect and retrieve
	them, use:
<p>
EMBOSS data files are distributed with the application and stored
in the standard EMBOSS data directory, which is defined
by the EMBOSS environment variable EMBOSS_DATA.

<p>

To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:

<pre>

% embossdata -fetch -file Exxx.dat

</pre>
<p>

Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called
".embossdata". Files for all EMBOSS runs can be put in the user's home
directory, or again in a subdirectory called ".embossdata".

<p>
The directories are searched in the following order:

<ul>
   <li> . (your current directory)
   <li> .embossdata (under your current directory)
   <li> ~/ (your home directory)
   <li> ~/.embossdata
</ul>
<p>

   -->

None.













<H2>
    Notes
</H2>

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        Useful things you can do with this program.
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None.







<H2>
    References
</H2>

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        Bibliography for methods used.
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None.








<H2>
    Warnings
</H2>

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        Potentially stupid things the program will let you do.
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None.







<H2>
    Diagnostic Error Messages
</H2>

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        Error messages specific to this program, eg:
        "FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
   -->

None.







<H2>
    Exit status
</H2>

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        Description of the exit status for various error conditions
   -->

It always exits with status 0.








<H2>
    Known bugs
</H2>


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        Bugs noted but not yet fixed.
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None.








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<H2>
    See also
</H2>
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<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr><td><a href="embossdata.html">embossdata</a></td><td>Finds or fetches the data files read in by the EMBOSS programs</td></tr>
<tr><td><a href="embossversion.html">embossversion</a></td><td>Writes the current EMBOSS version number</td></tr>
</table>

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        Add any comments about other associated programs (to prepare
        data files?) that seealso doesn't find. 
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<H2>
    Author(s)
</H2>
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        Who has worked on the program in the past.
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This application was written by Alan Bleasby <a
href="mailto:ableasby@hgmp.mrc.ac.uk">(ableasby@hgmp.mrc.ac.uk)</a>

















<H2>
    History
</H2>

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        What changes have been made.
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Written (March 2002) - Alan Bleasby.














<H2>
    Target users
</H2>

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        For general users, requested by one user, for EMBOSS site
        maintainers, for EMBOSS developers etc.
        eg:
        "This program is intended to be used by everyone and everything,
        from naive users to embedded scripts." 
	Which is easy to include using:
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Administrators of Jemboss servers only.











<H2>
    Comments
</H2>

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	Any comments, requests etc. that people have about the program
   -->








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