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-scal e 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 sm all-scale queries only. das sequence features Sequence Features OK - - 1222 /homes/pmr/local/share/EMBOSS/server.dasregistry http://www.dasregi stry.org/das/ DAS sequence/feature sources listed on the DAS re gistry tdas sequence features Sequence Features OK - - 1222 /homes/pmr/.embossdata/qatests.server.dasregistry http://www.d asregistry.org/das/ sequence/feature sources listed on dasregis try.org tensembldasserver sequence features Sequence Features OK - - 220 /homes/pmr/.embossdata/qatests.server.ensembldasserver http://www.e nsembl.org/das/ sequence/feature sources on ensembl das ser ver 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.e bi.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.e bi.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.e bi.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 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 (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