cacheensembl

 

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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
ictidomys_tridecemlineatus
ictidomys_tridecemlineatus_otherfeatures
latimeria_chalumnae
latimeria_chalumnae_otherfeatures
loxodonta_africana
macaca_mulatta
macaca_mulatta_otherfeatures
macaca_mulatta_variation
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
oreochromis_niloticus
oreochromis_niloticus_otherfeatures
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
pelodiscus_sinensis
pelodiscus_sinensis_otherfeatures
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
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:6.6.0.0

   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

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 2013-07-15 12:00:00
# Automatically generated by cacheensembl for server 'ensembl'.

DBNAME ailuropoda_melanoleuca [
  dbalias: "ailuropoda_melanoleuca_core_68_1"
  release: "68"
  server:  "ensembl"
  special: "SpeciesPrefix=ENSAME;"
]

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 [
  dbalias: "ailuropoda_melanoleuca_otherfeatures_68_1"
  release: "68"
  server:  "ensembl"
  special: "SpeciesPrefix=ENSAME;"
]

DBNAME anolis_carolinensis [
  dbalias: "anolis_carolinensis_core_68_2"
  release: "68"
  server:  "ensembl"
  special: "SpeciesPrefix=ENSACA;"
]

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 [
  dbalias: "anolis_carolinensis_otherfeatures_68_2"
  release: "68"
  server:  "ensembl"
  special: "SpeciesPrefix=ENSACA;"
]

DBNAME bos_taurus [
  dbalias: "bos_taurus_core_68_31"
  release: "68"
  server:  "ensembl"


  [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 [
  dbalias: "vicugna_pacos_core_68_1"
  release: "68"
  server:  "ensembl"
  special: "SpeciesPrefix=ENSVPA;"
]

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 [
  dbalias: "xenopus_tropicalis_core_68_42"
  release: "68"
  server:  "ensembl"
  special: "SpeciesPrefix=ENSXET;"
]

ALIAS 8364 xenopus_tropicalis
ALIAS xenopus xenopus_tropicalis
ALIAS xentro xenopus_tropicalis
ALIAS xtro xenopus_tropicalis
ALIAS xtropicalis xenopus_tropicalis

DBNAME xenopus_tropicalis_otherfeatures [
  dbalias: "xenopus_tropicalis_otherfeatures_68_42"
  release: "68"
  server:  "ensembl"
  special: "SpeciesPrefix=ENSXET;"
]

DBNAME xenopus_tropicalis_funcgen [
  dbalias: "xenopus_tropicalis_funcgen_68_42"
  release: "68"
  server:  "ensembl"
]

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