cacheensembl 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 Generates server cache file for an Ensembl server Description Contacts the ENSEMBL server to find the available databases and saves definitions for them to a server cache file. Usage Here is a sample session with cacheensembl % cacheensembl -servername ensembl -cachefile ~/.embossdata/qatests.server.ensem bl -auto ailuropoda_melanoleuca ailuropoda_melanoleuca_otherfeatures anolis_carolinensis anolis_carolinensis_otherfeatures bos_taurus bos_taurus_otherfeatures bos_taurus_variation bos_taurus_funcgen caenorhabditis_elegans caenorhabditis_elegans_funcgen callithrix_jacchus callithrix_jacchus_otherfeatures canis_familiaris canis_familiaris_otherfeatures canis_familiaris_variation canis_familiaris_funcgen cavia_porcellus cavia_porcellus_otherfeatures choloepus_hoffmanni ciona_intestinalis ciona_intestinalis_otherfeatures ciona_intestinalis_funcgen ciona_savignyi ciona_savignyi_otherfeatures danio_rerio danio_rerio_vega danio_rerio_otherfeatures danio_rerio_variation danio_rerio_funcgen dasypus_novemcinctus default_compara default_ontology dipodomys_ordii drosophila_melanogaster drosophila_melanogaster_otherfeatures drosophila_melanogaster_variation drosophila_melanogaster_funcgen echinops_telfairi equus_caballus equus_caballus_otherfeatures equus_caballus_variation erinaceus_europaeus felis_catus felis_catus_variation gallus_gallus gallus_gallus_otherfeatures gallus_gallus_variation gallus_gallus_funcgen gasterosteus_aculeatus gasterosteus_aculeatus_otherfeatures gorilla_gorilla gorilla_gorilla_otherfeatures homo_sapiens homo_sapiens_vega homo_sapiens_otherfeatures homo_sapiens_cdna homo_sapiens_variation homo_sapiens_funcgen loxodonta_africana macaca_mulatta macaca_mulatta_otherfeatures macaca_mulatta_funcgen macropus_eugenii meleagris_gallopavo meleagris_gallopavo_otherfeatures microcebus_murinus monodelphis_domestica monodelphis_domestica_variation mus_musculus mus_musculus_vega mus_musculus_otherfeatures mus_musculus_cdna mus_musculus_variation mus_musculus_funcgen myotis_lucifugus nomascus_leucogenys nomascus_leucogenys_otherfeatures ochotona_princeps ornithorhynchus_anatinus ornithorhynchus_anatinus_otherfeatures ornithorhynchus_anatinus_variation ornithorhynchus_anatinus_funcgen oryctolagus_cuniculus oryctolagus_cuniculus_otherfeatures oryzias_latipes oryzias_latipes_otherfeatures otolemur_garnettii pan_troglodytes pan_troglodytes_otherfeatures pan_troglodytes_variation pan_troglodytes_funcgen pongo_abelii pongo_abelii_otherfeatures pongo_abelii_variation procavia_capensis pteropus_vampyrus rattus_norvegicus rattus_norvegicus_otherfeatures rattus_norvegicus_variation rattus_norvegicus_funcgen saccharomyces_cerevisiae saccharomyces_cerevisiae_otherfeatures saccharomyces_cerevisiae_variation saccharomyces_cerevisiae_funcgen sorex_araneus spermophilus_tridecemlineatus sus_scrofa sus_scrofa_otherfeatures sus_scrofa_variation sus_scrofa_funcgen taeniopygia_guttata taeniopygia_guttata_otherfeatures taeniopygia_guttata_variation takifugu_rubripes takifugu_rubripes_otherfeatures tarsius_syrichta tetraodon_nigroviridis tetraodon_nigroviridis_otherfeatures tetraodon_nigroviridis_variation tupaia_belangeri tursiops_truncatus vicugna_pacos xenopus_tropicalis xenopus_tropicalis_otherfeatures xenopus_tropicalis_funcgen Go to the output files for this example Command line arguments Generates server cache file for an Ensembl server Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: -servername string Server name (Any string) [-cachefile] outfile [server.$(servername)] Server cache output file Additional (Optional) qualifiers: -outfile outfile [stdout] Output file name Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outfile" associated qualifiers -odirectory string Output directory "-cachefile" associated qualifiers -odirectory1 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 cacheensemblcontacts the ENSEMBL server for details of available databases. Output file format cacheensembl writes a server cache file which can be saved in the user's .embossdata directory or, for a system administrator, stored in the site-wide share/EMBOSS/ directory. Output files for usage example File: qatests.server.ensembl # /homes/pmr/.embossdata/qatests.server.ensembl 2011-07-15 12:00:00 # Automatically generated by cacheensembl for server 'ensembl'. DBNAME ailuropoda_melanoleuca [ release: "62" server: "ensembl" url: "mysql://anonymous@ensembldb.ensembl.org:5306/ailuropoda_melanoleuca_ core_62_1b" ] ALIAS 9646 ailuropoda_melanoleuca ALIAS ailmel ailuropoda_melanoleuca ALIAS ailmel1 ailuropoda_melanoleuca ALIAS amel ailuropoda_melanoleuca ALIAS amelanoleuca ailuropoda_melanoleuca ALIAS panda ailuropoda_melanoleuca DBNAME ailuropoda_melanoleuca_otherfeatures [ release: "62" server: "ensembl" url: "mysql://anonymous@ensembldb.ensembl.org:5306/ailuropoda_melanoleuca_ otherfeatures_62_1b" ] DBNAME anolis_carolinensis [ release: "62" server: "ensembl" url: "mysql://anonymous@ensembldb.ensembl.org:5306/anolis_carolinensis_cor e_62_2a" ] ALIAS 28377 anolis_carolinensis ALIAS acar anolis_carolinensis ALIAS acarolinensis anolis_carolinensis ALIAS anocar anolis_carolinensis ALIAS anolis anolis_carolinensis ALIAS anoliscarolinensis anolis_carolinensis ALIAS anolis_lizard anolis_carolinensis DBNAME anolis_carolinensis_otherfeatures [ release: "62" server: "ensembl" url: "mysql://anonymous@ensembldb.ensembl.org:5306/anolis_carolinensis_oth erfeatures_62_2a" ] DBNAME bos_taurus [ release: "62" server: "ensembl" url: "mysql://anonymous@ensembldb.ensembl.org:5306/bos_taurus_core_62_4k" ] ALIAS 9913 bos_taurus ALIAS bostau bos_taurus [Part of this file has been deleted for brevity] release: "62" server: "ensembl" url: "mysql://anonymous@ensembldb.ensembl.org:5306/tursiops_truncatus_core _62_1h" ] ALIAS 9739 tursiops_truncatus ALIAS dolphin tursiops_truncatus ALIAS ttru tursiops_truncatus ALIAS ttruncatus tursiops_truncatus ALIAS tursiopstruncatus tursiops_truncatus ALIAS turtru tursiops_truncatus ALIAS turtru1 tursiops_truncatus DBNAME vicugna_pacos [ release: "62" server: "ensembl" url: "mysql://anonymous@ensembldb.ensembl.org:5306/vicugna_pacos_core_62_1 h" ] ALIAS 30538 vicugna_pacos ALIAS alpaca vicugna_pacos ALIAS vicpac vicugna_pacos ALIAS vicpac1 vicugna_pacos ALIAS vicugnapacos vicugna_pacos ALIAS vpac vicugna_pacos ALIAS vpacos vicugna_pacos DBNAME xenopus_tropicalis [ release: "62" server: "ensembl" url: "mysql://anonymous@ensembldb.ensembl.org:5306/xenopus_tropicalis_core _62_42" ] ALIAS 8364 xenopus_tropicalis ALIAS xenopus xenopus_tropicalis ALIAS xentro xenopus_tropicalis ALIAS xtro xenopus_tropicalis ALIAS xtropicalis xenopus_tropicalis DBNAME xenopus_tropicalis_otherfeatures [ release: "62" server: "ensembl" url: "mysql://anonymous@ensembldb.ensembl.org:5306/xenopus_tropicalis_othe rfeatures_62_42" ] DBNAME xenopus_tropicalis_funcgen [ release: "62" server: "ensembl" url: "mysql://anonymous@ensembldb.ensembl.org:5306/xenopus_tropicalis_func gen_62_42" ] Data files **************** EDIT HERE **************** 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 dbtell Display information about a public database servertell Display information about a public server showdb Displays information on configured databases showserver Displays information on configured servers Author(s) Michael Schuster 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