                                 showserver



Wiki

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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Display 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
Display information on configured servers

# Name            Scope                      Type                       ID  Qry
All Count Cachefile                                              URL
                                  Comment
# =============== ========================== ========================== ==  ===
=== ===== ================================================== ===================
============================= =======
biomart           sequence                   Sequence                   OK  -
-     158 /homes/user/local/share/EMBOSS/server.biomart           http://www.bio
mart.org:80/biomart/martservice
ensembl           sequence                   Sequence                   OK  -
-     134 /homes/user/local/share/EMBOSS/server.ensembl           mysql://anonym
ous@ensembldb.ensembl.org:5306/    Public Ensembl MySQL instance, use for small-
scale queries only.
ensemblgenomes    sequence                   Sequence                   OK  -
-     476 /homes/user/local/share/EMBOSS/server.ensemblgenomes    mysql://anonym
ous@mysql.ebi.ac.uk:4157/          Public Ensembl Genomes MySQL instance, use fo
r small-scale queries only.
das               sequence features          Sequence Features          OK  -
-    1222 /homes/user/local/share/EMBOSS/server.dasregistry       http://www.das
registry.org/das/                  DAS sequence/feature sources listed on the DA
S registry
tdas              sequence features          Sequence Features          OK  -
-    1525 /homes/user/.embossdata/qatests.server.dasregistry      http://www.das
registry.org/das/                  sequence/feature sources listed on dasregistr
y.org
tensembldasserver sequence features          Sequence Features          OK  -
-     238 /homes/user/.embossdata/qatests.server.ensembldasserver http://www.ens
embl.org/das/                      sequence/feature sources on ensembl das serve
r
dbfetch           sequence features text obo Sequence Features Text Obo OK  -
-      49 /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.dkf
z.de/menu/cgi-bin/srs7.1.3.1/wgetz SRS from DKFZ Heidelberg
tdbfetch          sequence features text obo Sequence Features Text Obo OK  -
-      50 /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  -
-      50 /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  -
-      49 /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 search
ing across EBI public databases
tebeye            text                       Text                       OK  OK
-      65 /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.cmb
i.ru.nl/mrs-5/search
mrs3              text                       Unknown                    OK  OK
-      33 /homes/user/local/share/EMBOSS/server.mrs3              http://mrs.cmb
i.ru.nl/mrs-3/plain.do
mrs4              text                       Unknown                    OK  OK
-      33 /homes/user/local/share/EMBOSS/server.mrs4              http://mrs.cmb
i.ru.nl/mrs-web/plain.do
srs               text                       Unknown                    OK  OK
OK     21 /homes/user/local/share/EMBOSS/server.srs               http://srs.ebi
.ac.uk/srsbin/cgi-bin/wgetz        SRS from EBI


Command line arguments

Display information on configured servers
Version: EMBOSS:6.5.6.0

   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


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         Generate server cache file for DAS servers or for the DAS
                    registry
   cachedbfetch     Generate server cache file for Dbfetch/WSDbfetch data
                    sources
   cacheebeyesearch Generate server cache file for EB-eye search domains
   cacheensembl     Generate server cache file for an Ensembl server
   dbtell           Display information about a public database
   servertell       Display information about a public server
   showdb           Display 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 (c) 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
