EMBOSS: cacheensembl

| 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

Generate 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.ensembl -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
    gadus_morhua
    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
    latimeria_chalumnae
    latimeria_chalumnae_otherfeatures
    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
    myotis_lucifugus_otherfeatures
    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
    otolemur_garnettii_otherfeatures
    pan_troglodytes
    pan_troglodytes_otherfeatures
    pan_troglodytes_variation
    pan_troglodytes_funcgen
    petromyzon_marinus
    petromyzon_marinus_otherfeatures
    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
    sarcophilus_harrisii
    sarcophilus_harrisii_otherfeatures
    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

    Generate server cache file for an Ensembl server
    Version: EMBOSS:6.5.6.0

       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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
-servername | string | Server name | Any string |
[-cachefile] (Parameter 1) | outfile | Server cache output file | Output file | server.$(servername)
Additional (Optional) qualifiers
-outfile | outfile | Output file name | Output file | stdout
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
"-cachefile" associated outfile qualifiers
-odirectory1 -odirectory_cachefile | 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

## 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/user/.embossdata/qatests.server.ensembl 2012-07-15 12:00:00
    # Automatically generated by cacheensembl for server 'ensembl'.

    DBNAME ailuropoda_melanoleuca [
      release: "66"
      server:  "ensembl"
      special: "SpeciesPrefix=ENSAME;"
      url:     "mysql://anonymous@ensembldb.ensembl.org:5306/ailuropoda_melanoleuca_core_66_1"
    ]

    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: "66"
      server:  "ensembl"
      special: "SpeciesPrefix=ENSAME;"
      url:     "mysql://anonymous@ensembldb.ensembl.org:5306/ailuropoda_melanoleuca_otherfeatures_66_1"
    ]

    DBNAME anolis_carolinensis [
      release: "66"
      server:  "ensembl"
      special: "SpeciesPrefix=ENSACA;"
      url:     "mysql://anonymous@ensembldb.ensembl.org:5306/anolis_carolinensis_core_66_2"
    ]

    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: "66"
      server:  "ensembl"
      special: "SpeciesPrefix=ENSACA;"
      url:     "mysql://anonymous@ensembldb.ensembl.org:5306/anolis_carolinensis_otherfeatures_66_2"
    ]

    DBNAME bos_taurus [
      release: "66"
      server:  "ensembl"
      special: "SpeciesPrefix=ENSBTA;"

      [Part of this file has been deleted for brevity]

    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: "66"
      server:  "ensembl"
      special: "SpeciesPrefix=ENSVPA;"
      url:     "mysql://anonymous@ensembldb.ensembl.org:5306/vicugna_pacos_core_66_1"
    ]

    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: "66"
      server:  "ensembl"
      special: "SpeciesPrefix=ENSXET;"
      url:     "mysql://anonymous@ensembldb.ensembl.org:5306/xenopus_tropicalis_core_66_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: "66"
      server:  "ensembl"
      special: "SpeciesPrefix=ENSXET;"
      url:     "mysql://anonymous@ensembldb.ensembl.org:5306/xenopus_tropicalis_otherfeatures_66_42"
    ]

    DBNAME xenopus_tropicalis_funcgen [
      release: "66"
      server:  "ensembl"
      special: ""
      url:     "mysql://anonymous@ensembldb.ensembl.org:5306/xenopus_tropicalis_funcgen_66_42"
    ]

## 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
dbtell | Display information about a public database
servertell | Display information about a public server
showdb | Display information on configured databases
showserver | Display 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 © 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