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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: showserver
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
showserver
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Display information on configured servers
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>
    Description
</H2>

<p><b>showserver</b> displays a table with the names, contents and access methods of the sequence servers configured for your EMBOSS installation.</p>

<H2>
    Usage
</H2>

<!--  
	Example usage, as run from the command-line.
        Many examples illustrating different behaviours is good.
 -->

Here is a sample session with <b>showserver</b>
<p>
Display information on the currently available servers: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showserver </b>
Display information on configured servers

# Name            Scope                      Type                       ID  Qry All Count Cachefile                                             URL                                              Comment
# =============== ========================== ========================== ==  === === ===== ===================================================== ================================================ =======
biomart           sequence                   Sequence                   OK  OK  -     158 /homes/user/local/share/EMBOSS/server.biomart           http://www.biomart.org:80/biomart/martservice    
ensembl           sequence                   Sequence                   OK  OK  -     140 /homes/user/local/share/EMBOSS/server.ensembl           mysql://anonymous@ensembldb.ensembl.org:5306/    Public Ensembl MySQL instance, use for small-scale queries only.
ensemblgenomes    sequence                   Sequence                   OK  OK  -     496 /homes/user/local/share/EMBOSS/server.ensemblgenomes    mysql://anonymous@mysql.ebi.ac.uk:4157/          Public Ensembl Genomes MySQL instance, use for small-scale queries only.
das               sequence features          Sequence Features          OK  OK  -    1222 /homes/user/local/share/EMBOSS/server.dasregistry       http://www.dasregistry.org/das/                  DAS sequence/feature sources listed on the DAS registry
tdas              sequence features          Sequence Features          OK  OK  -    1530 /homes/user/.embossdata/qatests.server.dasregistry      http://www.dasregistry.org/das/                  sequence/feature sources listed on dasregistry.org
tensembldasserver sequence features          Sequence Features          OK  OK  -     249 /homes/user/.embossdata/qatests.server.ensembldasserver http://www.ensembl.org/das/                      sequence/feature sources on ensembl das server
dbfetch           sequence features text obo Sequence Features Text Obo OK  -   -      50 /homes/user/local/share/EMBOSS/server.dbfetch           http://www.ebi.ac.uk/Tools/dbfetch/              EBI dbfetch webservices(REST)
dkfz              sequence features text obo Sequence Features Text Obo OK  OK  OK      1 /homes/user/local/share/EMBOSS/server.dkfz              http://www.dkfz.de/menu/cgi-bin/srs7.1.3.1/wgetz SRS from DKFZ Heidelberg
tdbfetch          sequence features text obo Sequence Features Text Obo OK  -   -      46 /homes/user/.embossdata/qatests.server.tdbfetch         http://www.ebi.ac.uk/Tools/dbfetch/              EBI dbfetch webservices(REST)
twsdbfetch        sequence features text obo Sequence Features Text Obo OK  -   -      46 /homes/user/.embossdata/qatests.server.twsdbfetch       http://www.ebi.ac.uk/ws/services/WSDbfetchDoclit EBI dbfetch webservices(SOAP)
wsdbfetch         sequence features text obo Sequence Features Text Obo OK  -   -      50 /homes/user/local/share/EMBOSS/server.wsdbfetch         http://www.ebi.ac.uk/ws/services/WSDbfetchDoclit EBI dbfetch webservices(SOAP)
ebeye             text                       Text                       OK  OK  -      62 /homes/user/local/share/EMBOSS/server.ebeye             http://www.ebi.ac.uk/ebisearch/service.ebi       EB-eye text search service that allows searching across EBI public databases
tebeye            text                       Text                       OK  OK  -      80 /homes/user/.embossdata/qatests.server.ebeye            http://www.ebi.ac.uk/ebisearch/service.ebi       EBI ebeye webservices
entrez            text                       Unknown                    OK  OK  -      48 /homes/user/local/share/EMBOSS/server.entrez                                                             
mrs               text                       Unknown                    OK  OK  -      33 /homes/user/local/share/EMBOSS/server.mrs               http://mrs.cmbi.ru.nl/mrs-5/search               
mrs3              text                       Unknown                    OK  OK  -      33 /homes/user/local/share/EMBOSS/server.mrs3              http://mrs.cmbi.ru.nl/mrs-3/plain.do             
mrs4              text                       Unknown                    OK  OK  -      33 /homes/user/local/share/EMBOSS/server.mrs4              http://mrs.cmbi.ru.nl/mrs-web/plain.do           
srs               text                       Unknown                    OK  OK  OK     16 /homes/user/local/share/EMBOSS/server.srs               http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz        SRS from EBI

</pre></td></tr></table><p>
<p>
<p>



<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Display information on configured servers
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers:
   -servername         string     Name of a single server to give information
                                  on (Any string)
   -showtypes          menu       [*] Show type(s) (Values: Protein (Protein
                                  sequences); Nucleic (Nucleotide sequences);
                                  Sequence (Any sequence data); Protfeatures
                                  (Protein features); Nucfeatures (Nucleotide
                                  features); Features (Any feature table
                                  data); Obo (OBO ontology data); Resource
                                  (Data resource); Taxonomy (Taxonomy data);
                                  Assembly (Assembled short read data); Text
                                  (text data); Html (HTML text data); Xml (XML
                                  text data); Unknown (Unspecified datatype
                                  to be defined for each database))
   -html               boolean    [N] Format output as an HTML table
   -full               boolean    [N] Display all columns
   -methods            boolean    [$(full)] This displays the access methods
                                  that can be used on this server, for all,
                                  query or ID access
   -[no]count          boolean    [Y] Display 'count' column
   -[no]cachefile      boolean    [Y] Display 'cachefile' column
   -[no]url            boolean    [Y] Display 'URL' column
   -fields             boolean    [$(full)] This displays the search fields
                                  that can be used on this server, other than
                                  the standard 'id' or 'acc' fields.
   -defined            boolean    [$(full)] This displays a short name for the
                                  file containing the server definition
   -serverversion      boolean    [$(full)] Display 'version' column
   -sortby             menu       [type] Sort by (Values: defined (Definition
                                  file short name); type (Datatype))
   -outfile            outfile    [stdout] Output file name

   Advanced (Unprompted) qualifiers:
   -only               toggle     [N] This is a way of shortening the command
                                  line if you only want a few standard columns
                                  to be displayed. Instead of specifying:
                                  '-nohead -notype -noid -noquery -noall'
                                  to get only the comment output, you can
                                  specify
                                  '-only -comment'
   -heading            boolean    [@(!$(only))] Display column headings
   -scope              boolean    [@(!$(only))] Display 'scope' column
   -type               boolean    [@(!$(only))] Display 'type' column
   -id                 boolean    [@(!$(only))] Display 'id' column
   -query              boolean    [@(!$(only))] Display 'qry' column
   -all                boolean    [@(!$(only))] Display 'all' column
   -comment            boolean    [@(!$(only))] Display 'comment' column

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-servername</td>
<td>string</td>
<td>Name of a single server to give information on</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-showtypes</td>
<td>list</td>
<td>Show type(s)</td>
<td><table><tr><td>Protein</td> <td><i>(Protein sequences)</i></td></tr><tr><td>Nucleic</td> <td><i>(Nucleotide sequences)</i></td></tr><tr><td>Sequence</td> <td><i>(Any sequence data)</i></td></tr><tr><td>Protfeatures</td> <td><i>(Protein features)</i></td></tr><tr><td>Nucfeatures</td> <td><i>(Nucleotide features)</i></td></tr><tr><td>Features</td> <td><i>(Any feature table data)</i></td></tr><tr><td>Obo</td> <td><i>(OBO ontology data)</i></td></tr><tr><td>Resource</td> <td><i>(Data resource)</i></td></tr><tr><td>Taxonomy</td> <td><i>(Taxonomy data)</i></td></tr><tr><td>Assembly</td> <td><i>(Assembled short read data)</i></td></tr><tr><td>Text</td> <td><i>(text data)</i></td></tr><tr><td>Html</td> <td><i>(HTML text data)</i></td></tr><tr><td>Xml</td> <td><i>(XML text data)</i></td></tr><tr><td>Unknown</td> <td><i>(Unspecified datatype to be defined for each database)</i></td></tr></table></td>
<td>*</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-html</td>
<td>boolean</td>
<td>Format output as an HTML table</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-full</td>
<td>boolean</td>
<td>Display all columns</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-methods</td>
<td>boolean</td>
<td>This displays the access methods that can be used on this server, for all, query or ID access</td>
<td>Boolean value Yes/No</td>
<td>$(full)</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]count</td>
<td>boolean</td>
<td>Display 'count' column</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]cachefile</td>
<td>boolean</td>
<td>Display 'cachefile' column</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]url</td>
<td>boolean</td>
<td>Display 'URL' column</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-fields</td>
<td>boolean</td>
<td>This displays the search fields that can be used on this server, other than the standard 'id' or 'acc' fields.</td>
<td>Boolean value Yes/No</td>
<td>$(full)</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-defined</td>
<td>boolean</td>
<td>This displays a short name for the file containing the server definition</td>
<td>Boolean value Yes/No</td>
<td>$(full)</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-serverversion</td>
<td>boolean</td>
<td>Display 'version' column</td>
<td>Boolean value Yes/No</td>
<td>$(full)</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-sortby</td>
<td>list</td>
<td>Sort by</td>
<td><table><tr><td>defined</td> <td><i>(Definition file short name)</i></td></tr><tr><td>type</td> <td><i>(Datatype)</i></td></tr></table></td>
<td>type</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-outfile</td>
<td>outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td>stdout</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-only</td>
<td>toggle</td>
<td>This is a way of shortening the command line if you only want a few standard columns to be displayed. Instead of specifying:
'-nohead -notype -noid -noquery -noall'
to get only the comment output, you can specify
'-only -comment'</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-heading</td>
<td>boolean</td>
<td>Display column headings</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-scope</td>
<td>boolean</td>
<td>Display 'scope' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-type</td>
<td>boolean</td>
<td>Display 'type' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-id</td>
<td>boolean</td>
<td>Display 'id' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-query</td>
<td>boolean</td>
<td>Display 'qry' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-all</td>
<td>boolean</td>
<td>Display 'all' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-comment</td>
<td>boolean</td>
<td>Display 'comment' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->








<H2>
    Input file format
</H2>


<b>showserver</b> examines the database servers defined for this
EMBOSS installation and for the current user.

<p>






<H2>
    Output file format
</H2>



<p>

The output is a simple text table.




<H2>
    Data files
</H2>

None.


<H2>
    Notes
</H2>

<!-- 
        Restrictions.
        Interesting behaviour.
        Useful things you can do with this program.
   -->

None.







<H2>
    References
</H2>

<!-- 
        Bibliography for methods used.
<ol>

<li>

</ol>

   -->

None.








<H2>
    Warnings
</H2>

<!-- 
        Potentially stupid things the program will let you do.
   -->

None.







<H2>
    Diagnostic Error Messages
</H2>

<!-- 
        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>

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

It always exits with status 0.








<H2>
    Known bugs
</H2>


<!-- 
        Bugs noted but not yet fixed.
   -->

None.








<!--
<H2>
    See also
</H2>
-->
<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="cachedas.html">cachedas</a></td>
<td>Generate server cache file for DAS servers or for the DAS registry</td>
</tr>

<tr>
<td><a href="cachedbfetch.html">cachedbfetch</a></td>
<td>Generate server cache file for Dbfetch/WSDbfetch data sources</td>
</tr>

<tr>
<td><a href="cacheebeyesearch.html">cacheebeyesearch</a></td>
<td>Generate server cache file for EB-eye search domains</td>
</tr>

<tr>
<td><a href="cacheensembl.html">cacheensembl</a></td>
<td>Generate server cache file for an Ensembl server</td>
</tr>

<tr>
<td><a href="dbtell.html">dbtell</a></td>
<td>Display information about a public database</td>
</tr>

<tr>
<td><a href="servertell.html">servertell</a></td>
<td>Display information about a public server</td>
</tr>

<tr>
<td><a href="showdb.html">showdb</a></td>
<td>Display information on configured databases</td>
</tr>

</table>
<!-- 
        Add any comments about other associated programs (to prepare
        data files?) that seealso doesn't find. 
   -->










<H2>
    Author(s)
</H2>

Peter Rice
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
<H2>
    History
</H2>
<!--
        Date written and what changes have been made go in this file.
   -->




<H2>
    Target users
</H2>
<!--
        For general users, use this text
   -->
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
<!--
        User/developer/other comments go in this file.
   -->
None


</BODY>
</HTML>