|   | showserver | 
Please help by correcting and extending the Wiki pages.
showserver displays a table with the names, contents and access methods of the sequence servers configured for your EMBOSS installation.
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 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 | 
| 
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
 | 
| Qualifier | Type | Description | Allowed values | Default | ||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||||||||||||||||||||||
| (none) | ||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||||||||||||||||
| -servername | string | Name of a single server to give information on | Any string | |||||||||||||||||||||||||||||
| -showtypes | list | Show type(s) | 
 | * | ||||||||||||||||||||||||||||
| -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 | $(full) | ||||||||||||||||||||||||||||
| -sortby | list | Sort by | 
 | type | ||||||||||||||||||||||||||||
| -outfile | outfile | Output file name | Output file | stdout | ||||||||||||||||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||||||||||||||||
| -only | toggle | This is a way of shortening the command line if you only want a few standard columns to be displayed. Instead of specifying: '-nohead -notype -noid -noquery -noall' to get only the comment output, you can specify '-only -comment' | Toggle value Yes/No | No | ||||||||||||||||||||||||||||
| -heading | boolean | Display column headings | Boolean value Yes/No | @(!$(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 | ||||||||||||||||||||||||||||
The output is a simple text table.
| 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 | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.