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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
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 OK
- 158 /homes/user/local/share/EMBOSS/server.biomart http://www.bio
mart.org:80/biomart/martservice
ensembl sequence Sequence OK OK
- 140 /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 OK
- 496 /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 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 OK
- 1530 /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 OK
- 249 /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 -
- 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.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 -
- 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 search
ing 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.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 16 /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:6.6.0.0
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
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
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