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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
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| 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.