showserver

 

Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

Function

Displays information on configured servers

Description

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

Usage

Here is a sample session with showserver

Display information on the currently available servers: 


% showserver 
Displays information on configured servers

# Name            Scope                      Type                       ID  Qry All Count Cachefile                                              URL                                              Comment
# =============== ========================== ========================== ==  === === ===== ================================================== ================================================ =======
biomart           sequence                   Sequence                   OK  -   -     158 /homes/pmr/local/share/EMBOSS/server.biomart           http://www.biomart.org:80/biomart/martservice    
ensembl           sequence                   Sequence                   OK  -   -     125 /homes/pmr/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  -   -     441 /homes/pmr/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  -   -    1222 /homes/pmr/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  -   -     904 /homes/pmr/.embossdata/qatests.server.dasregistry      http://www.dasregistry.org/das/                  sequence/feature sources listed on dasregistry.org
tensembldasserver sequence features          Sequence Features          OK  -   -     220 /homes/pmr/.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  -   -      45 /homes/pmr/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/pmr/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  -   -      45 /homes/pmr/.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  -   -      45 /homes/pmr/.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  -   -      45 /homes/pmr/local/share/EMBOSS/server.wsdbfetch         http://www.ebi.ac.uk/ws/services/WSDbfetchDoclit EBI dbfetch webservices(SOAP)
ebeye             text                       Text                       OK  OK  -      62 /homes/pmr/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  -      62 /homes/pmr/.embossdata/qatests.server.ebeye            http://www.ebi.ac.uk/ebisearch/service.ebi       EBI ebeye webservices
entrez            text                       Unknown                    OK  OK  -      47 /homes/pmr/local/share/EMBOSS/server.entrez                                                             
mrs               text                       Unknown                    OK  OK  -      33 /homes/pmr/local/share/EMBOSS/server.mrs               http://mrs.cmbi.ru.nl/mrs-5/search               
mrs3              text                       Unknown                    OK  OK  -      33 /homes/pmr/local/share/EMBOSS/server.mrs3              http://mrs.cmbi.ru.nl/mrs-3/plain.do             
mrs4              text                       Unknown                    OK  OK  -      33 /homes/pmr/local/share/EMBOSS/server.mrs4              http://mrs.cmbi.ru.nl/mrs-web/plain.do           
srs               text                       Unknown                    OK  OK  OK     21 /homes/pmr/local/share/EMBOSS/server.srs               http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz       SRS from EBI

Command line arguments 

Displays information on configured servers
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers:
   -server             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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
(none)
Additional (Optional) qualifiers
-server string Name of a single server to give information on Any string  
-showtypes list Show type(s)
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 Format output as an HTML table Boolean value Yes/No No
-full boolean Display all columns Boolean value Yes/No No
-methods boolean This displays the access methods that can be used on this server, for all, query or ID access Boolean value Yes/No $(full)
-[no]count boolean Display 'count' column Boolean value Yes/No Yes
-[no]cachefile boolean Display 'cachefile' column Boolean value Yes/No Yes
-[no]url boolean Display 'URL' column Boolean value Yes/No Yes
-fields boolean This displays the search fields that can be used on this server, other than the standard 'id' or 'acc' fields. Boolean value Yes/No $(full)
-defined boolean This displays a short name for the file containing the server definition Boolean value Yes/No $(full)
-serverversion boolean Display 'version' column Boolean value Yes/No $(full)
-sortby list Sort by
defined (Definition file short name)
type (Datatype)
 type
-outfile outfile Output file name Output file stdout
Advanced (Unprompted) qualifiers
-only toggle This is a way of shortening the command line if you only want a few standard columns to be displayed. Instead of specifying: '-nohead -notype -noid -noquery -noall' to get only the comment output, you can specify '-only -comment' Toggle value Yes/No No
-heading boolean Display column headings Boolean value Yes/No @(!$(only))
-scope boolean Display 'scope' column Boolean value Yes/No @(!$(only))
-type boolean Display 'type' column Boolean value Yes/No @(!$(only))
-id boolean Display 'id' column Boolean value Yes/No @(!$(only))
-query boolean Display 'qry' column Boolean value Yes/No @(!$(only))
-all boolean Display 'all' column Boolean value Yes/No @(!$(only))
-comment boolean Display 'comment' column Boolean value Yes/No @(!$(only))
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

showserver examines the database servers defined for this EMBOSS installation and for the current user.

Output file format

The output is a simple text table.

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
cachedas Generates server cache file for DAS servers or for the DAS registry
cachedbfetch Generates server cache file for Dbfetch/WSDbfetch data sources
cacheebeyesearch Generates server cache file for EB-eye search domains
cacheensembl Generates server cache file for an Ensembl server
dbtell Display information about a public database
servertell Display information about a public server
showdb Displays information on configured databases

Author(s)

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

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None