# tempdata - this is the directory used by the test databases TEMBL, TSW, etc.
# If you use these databases for testing you must uncomment this line and set
# the definition to the directory where the databases are installed.
# By default this is /usr/local/share/EMBOSS/test but the directory can
# be changed with --prefix when you configure EMBOSS.

# SET emboss_tempdata path_to_directory_$EMBOSS/test

# Proxy - set this if any databases are accessed through a proxy web server.
# Turn off in the DB definition with proxy: ":" for any
# databases that are internal and should not go through the proxy.

# SET emboss_proxy "proxy.mydomain.ac.uk:8080"

# Logfile - set this to a file that any user can append to
# and EMBOSS applications will automatically write log information

# SET emboss_logfile /packages/emboss/emboss/log

# Pagesize - this is the size of disc page blocks and is
# required by the 'dbx' indexing programs and 'method: emboss'
# We recommend a value of 2048

SET PAGESIZE 2048

# Cachesize - a cache of disc pages to be used by the 'dbx'
# indexing system and is required for 'method emboss'. It is
# the number of PAGESIZE blocks to cache. We recommend
# a value of 200

SET CACHESIZE 200

##################################################################
# Test Databases
# Used by the qatest.pl script to test an EMBOSS installation.
# Comment them out if you do not want your users to use them.
# Examples in the EMBOSS documentation should all run by using
# TEMBL: in place of EMBL:, TSW: in place of SW:, and so on.
##################################################################


# swissprot (Puffer fish entries)
# =========

DB tsw [ type: P dir: $emboss_tempdata/swiss
   method: emblcd format: swiss release: 36
   fields: "sv des org key"
   comment: "Swissprot native format with EMBL CD-ROM index" ]

# swnew (Puffer fish entries)
# =====

DB tswnew [ type: P dir: $emboss_tempdata/swnew
   method: emblcd format: swiss release: 37 
   fields: "sv des org key"
   comment: "Swissnew as 3 files in native format with EMBL CD-ROM index" ]

# wormpep (cosmid ZK637)
# =======

DB twp [ type: P dir: $emboss_tempdata/wormpep
   method: emblcd format: fasta release: 16 
   fields: "des"
   comment: "EMBL new in native format with EMBL CD-ROM index" ]

# embl (worm cosmid ZK637 and a few other entries)
# ====

DB tembl [ type: N dir: $emboss_tempdata/embl
   method: emblcd format: embl release: 57 
   fields: "sv des org key"
   comment: "EMBL in native format with EMBL CD-ROM index" ]

# pir (cytochrome C plus first entries in other divisions)
# ===

DB tpir [ type: P dir: $emboss_tempdata/pir
   method: gcg
   file: pir*.seq
   format: nbrf
   fields: "des org key"
   comment: "PIR using NBRF access for 4 files" ]

# Genbank (Canadian EMBnet node - so long as they are running SRS version 6)
# =======

DB tgb [ type: N method: srswww format: genbank
   url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz"
   dbalias: genbankrelease
   fields: "sv des org key"
   comment: "Genbank IDs" ]

# Genbank (local copy of the TEMBL entries from Genbank)
# =======

DB tgenbank [ type: N dir: $emboss_tempdata/genbank
   method: emblcd format: genbank release: 01 
   fields: "sv des org key"
   comment: "GenBank in native format with EMBL CD-ROM index" ]

#############################################
# DATABASE SETTING EXAMPLES
#
# Modify these for your own
# local and remote database definitions
#
# See the EMBOSS Administrators Guide 3.0.0
# for full documentation on DB definitions.
#############################################

#######################################################################
# GENBANK from the Canadian EMBnet node SRSWWW server
#######################################################################


#DB genbank [ type: N method: url format: genbank
#   url: "http://www.ca.embnet.org/srs6bin/cgi-bin/wgetz?-id+-e+[genbank-id:'%s']+-vn+2"
#   comment: "Genbank IDs" ]

#DB gb [ type: N method: url format: genbank
#   url: "http://www.ca.embnet.org/srs6bin/cgi-bin/wgetz?-id+-e+[genbank-id:'%s']+-vn+2"
#   comment: "Genbank IDs" ]

#DB genbanka [ type: N method: url format: genbank
#   url: "http://www.ca.embnet.org/srs6bin/cgi-bin/wgetz?-id+-e+[genbank-acc:'%s']+-vn+2"
#   comment: "Genbank ACs" ]

#DB gba [ type: N method: url format: genbank
#   url: "http://www.ca.embnet.org/srs6bin/cgi-bin/wgetz?-id+-e+[genbank-acc:'%s']+-vn+2"
#   comment: "Genbank ACs" ]

## N.B.
# For older SRS servers use e.g.
#DB gb [ type: N method: url format: genbank
#   url: "http://srs.csc.fi:8002/srs6bin/cgi-bin/wgetz?-e+[genbank-id:%s]"
#   comment: "Genbank IDs" ]




#######################################################################
# PIR/NBRF indexed with dbigcg
#######################################################################

# Set the directory to where the database is stored
# Assumed the dbigcg index files are in the same directory

# DB pir [ type: P dir: /data/pir
#    method: gcg
#    file: pir*.seq
#    format: nbrf
#    comment: "PIR/NBRF" ]

# DB nbrf [ type: P dir: /data/pir
#    method: gcg
#    file: pir*.seq
#    format: nbrf
#    comment: "PIR/NBRF" ]




##########################################################################
# SWISSPROT indexed with dbiflat
##########################################################################

# SWISSPROT: Set the directory to where the database is stored
# Assumed the dbiflat index files are in the same directory

# DB swissprot [ 
#         type: P 
#         comment: "SWISSPROT sequences"
#         method: emblcd
#         format: swiss 
#         dbalias: swissprot
#         dir: /data/swissprot/ 
#         file: seq.dat
# ]

# SWISSNEW: Set the directory to where the database is stored
# Assumed the dbiflat index files are in the same directory

# DB sw [ 
#         type: P 
#         comment: "SWISSPROT sequences"
#         method: emblcd
#         format: swiss 
#         dbalias: swissprot
#         dir: /data/swissprot/ 
#         file: seq.dat
# ]



#########################################################
# EMBL indexed with dbiflat
#########################################################

# EMBL: Set the directory to where the database is stored
# Assumed the dbiflat index files are in the same directory
# Second definition is another name for the first.

#DB embl [ type: N method: emblcd release: "61.0"
#         format: embl dir: /data/embl/
#         file: *.dat comment: "EMBL sequences"
#]

#DB em [ type: N method: emblcd release: "61.0"
#         format: embl dir: /data/embl/
#         file: *.dat comment: "EMBL sequences"
#]


## Old EMBL definitions (for historical reasons) using SRSWWW
##DB embla [ type: N method: url format: embl
##  url: "http://srs.hgmp.mrc.ac.uk/srs6bin/cgi-bin/wgetz?-e+[embl-acc:%s]"
##  comment: "Use embl instead!" ]
##
##DB ema [ type: N method: url format: embl
##  url: "http://srs.hgmp.mrc.ac.uk/srs6bin/cgi-bin/wgetz?-e+[embl-acc:%s]"
##  comment: "Use embl instead!" ]

#########################################################
# EMBL NEW
#########################################################

# EMBLNEW: Set the directory to where the database is stored
# Assumed the dbiflat index files are in the same directory

# DB emblnew [ type: N method: emblcd release: "0.0"
#          format: embl dir: /data/embl/newdata/
#          file: *.dat comment: "New EMBL sequences"
# ]



##########################################################
# EMBL subdivisions using the original EMBL dbiflat indices
##########################################################

# Simply redefine EMBL with exclude:  and file: to limit
# the database files available

# DB fungal [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */fun*.dat comment: "EMBL fungal sequences"
# ]

# DB est [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */est*.dat comment: "EMBL EST sequences"
# ]

# DB gss [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */gss*.dat comment: "EMBL GSS sequences"
# ]

# DB htg [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */htg*.dat comment: "EMBL HTG sequences"
# ]

# DB human [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */hum?.dat comment: "EMBL human sequences"
# ]

# DB humanest [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/est/ exclude: *.dat
#          file: */humanest*.dat comment: "EMBL human EST sequences"
# ]

# DB invertebrate [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */inv*.dat comment: "EMBL invertebrate sequences"
# ]

# DB mammalian [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */mam*.dat comment: "EMBL mammalian sequences"
# ]

# DB mouseest [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/est/ exclude: *.dat
#          file: */mouseest*.dat comment: "EMBL mouse EST sequences"
# ]

# DB organelle [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */org*.dat comment: "EMBL organelle sequences"
# ]

# DB otherest [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/est/ exclude: *.dat
#          file: */otherest*.dat comment: "EMBL other EST sequences"
# ]

# DB patent [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */patent*.dat comment: "EMBL patented sequences"
# ]

# DB phage [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */phg*.dat comment: "EMBL phage sequences"
# ]

# DB plant [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */pln*.dat comment: "EMBL plant sequences"
# ]

# DB prokaryotic [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */pro*.dat comment: "EMBL prokaryotic sequences"
# ]

# DB rodent [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */rod*.dat comment: "EMBL rodent sequences"
# ]

# DB sts [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */sts*.dat comment: "EMBL STS sequences"
# ]

# DB synthetic [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */syn*.dat comment: "EMBL synthetic sequences"
# ]

# DB unclassified [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */unc*.dat comment: "EMBL unclassified sequences"
# ]

# DB viral [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */vrl*.dat comment: "EMBL viral sequences"
# ]

# DB othervertebrate [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: */vrt*.dat comment: "EMBL other vertebrate sequences"
# ]

# DB vertebrate [ type: N method: emblcd release: "61.0"
#          format: embl dir: /data/embl/ exclude: *.dat
#          file: "*/vrt*.dat */mam*.dat */rod*.dat"
#          comment: "EMBL vertebrate sequences"
# ]


####################################################################
# TREMBL databases indexed with dbiflat
####################################################################

# TREMBL: Set the directory to where the database is stored
# Assumed the dbiflat index files are in the same directory

# DB trembl [ 
#         type: P 
#         comment: "TREMBL sequences"
#         method: emblcd
#         format: swiss 
#         dir: /data/trembl/ 
#         file: tr_*.dat
# ]

# SPTREMBL: Set the directory to where the database is stored
# Assumed the dbiflat index files are in the same directory

# DB sptrembl [ 
#         type: P 
#         comment: "SPTREMBL sequences"
#         method: emblcd
#         format: swiss 
#         dir: /data/trembl/sptrembl/
#         file: tr_*.dat
# ]

# DB remtrembl [ 
#         type: P 
#         comment: "REMTREMBL sequences"
#         method: emblcd
#         format: swiss 
#         dir: /data/trembl/sptrembl/
#         file: tr_*.dat
# ]



####################################################################
# New TREMBL
####################################################################

# TREMBLNEW: Set the directory to where the database is stored
# Assumed the dbiflat index files are in the same directory

# DB tremblnew [ 
#         type: P
#         comment: "New TREMBL sequences"
#         method: emblcd
#         format: swiss 
#         dir: /data/trembl/emboss/ 
#         file: tremblnew*.dat
# ]



####################################################################
# Trembl subsections
####################################################################

# Simply redefine TREMBL with exclude:  and file: to limit
# the database files available

# DB trarc [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_arc*.dat comment: "TREMBL ARC sequences"
# ]

# DB trfungal [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_fun*.dat comment: "TREMBL fungal sequences"
# ]

# DB trhuman [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_hum*.dat comment: "TREMBL human sequences"
# ]

# DB trimmuno [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_immuno*.dat comment: "TREMBL immunological sequences"
# ]

# DB trinvertebrate [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_inv*.dat comment: "TREMBL invertebrate sequences"
# ]

# DB trmammalian [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_mam*.dat comment: "TREMBL mammalian sequences"
# ]

# DB trmhc [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_mhc*.dat comment: "TREMBL MHC sequences"
# ]

# DB trorganelle [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_org*.dat comment: "TREMBL organelle sequences"
# ]

# DB trpatent [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_patent*.dat comment: "TREMBL patented sequences"
# ]

# DB trphage [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_phg*.dat comment: "TREMBL phage sequences"
# ]

# DB trplant [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_pln*.dat comment: "TREMBL plant sequences"
# ]

# DB trprokaryotic [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/embl/ exclude: *.dat
#          file: */tr_pro*.dat comment: "TREMBL prokaryotic sequences"
# ]

# DB trpseudo [ type: P method: emblcd release: "61.0"
#          format: embl dir: /data/trembl/ exclude: *.dat
#          file: */tr_pseudo*.dat comment: "TREMBL pseudo sequences"
# ]

# DB trrodent [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_rod*.dat comment: "TREMBL rodent sequences"
# ]

# DB trsmall [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_smalls*.dat comment: "TREMBL small sequences"
# ]

# DB trsynthetic [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_syn*.dat comment: "TREMBL synthetic sequences"
# ]

# DB trtruncated [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_truncated*.dat comment: "TREMBL truncated sequences"
# ]

# DB trunclassified [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_unc*.dat comment: "TREMBL unclassified sequences"
# ]

# DB trviral [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_vrl*.dat comment: "TREMBL viral sequences"
# ]

# DB trothervertebrate [ type: P method: emblcd release: "61.0"
#          format: swiss dir: /data/trembl/ exclude: *.dat
#          file: */tr_vrt*.dat comment: "TREMBL other vertebrate sequences"
# ]



####################################################################
# Biomart example
####################################################################

#DB martensembl [
#    method: "biomart"
#    type: "P"
#    url: "http://www.biomart.org:80/biomart/martservice"
# dbalias is the dataset
#    dbalias: "hsapiens_gene_ensembl"
#
# The format must be 'biomart'
#    format: "biomart"
#
# identifier is the biomart filter the query will be performed with
# e.g. seqret martensembl:ENST00000380152
#
#    identifier: "ensembl_transcript_id"
#
# Additional filters may be added here e.g.
#
#    filter: "chromosome_name=13"
#
# This is the biomart attribute specifying the sequence
# 
#    sequence: "peptide"
#
# These are fields you want returned as part of the description
#
#    return: "ensembl_gene_id,description,external_gene_id,chromosome_name"
#]



####################################################################
# SQL example (dummy)
####################################################################

#DB sqlexample [
#    method: "sql"
#    type: "N"
#
# method://username:password@host/databasename
#    url: "mysql://dummy:pass@machine.somedomain.org:3306/dummyseqs"
#
# dbalias is the table name containing the sequence information
#    dbalias: "sequences"
#
# The SQL data is processed using biomart format. That is not a typo.
#    format: "biomart"
#
# Column name containing IDs|Accs i.e. the column the query will be
# performed against
#    identifier: "accession"
#
# Any additional SQL restrictions can be put here e.g. 
#    filter: "AND version IS NOT NULL"
#
# Column containing sequence
#    sequence: "sequence"
#
# Columns you want to add to the description
#    return: "version,description"
#]



##################################################################
# Ensembl datatabase access example via public MySQL instances.
#
# Please note that these public MySQL instances are only provided
# for small-scale access. For extended analyses and if in doubt,
# please copy the relevant databases to a private MySQL instance
# and configure access accordingly. Please see the following
# instructions on how to setup your own MySQL server.
# http://www.ensembl.org/info/docs/webcode/install/build.html
##################################################################

# DB ensembl [
#   type:        "Nucleotide"
#   format:      "ensembl"
#   method:      "ensembl"
#   url:         "mysql://anonymous:@ensembldb.ensembl.org:5306/"
#   comment:     "Ensembl test database"
# ]
#
# DB ensemblgenomes [
#   type:        "Nucleotide"
#   format:      "ensembl"
#   method:      "ensembl"
#   url:         "mysql://anonymous:@mysql.ebi.ac.uk:4157/"
#   comment:     "Ensembl test database"
# ]



##################################################################
# Resource definitions for the dbx indexing system.
##################################################################
#
#RES embl [ type: Index
#  idlen:  15
#  acclen: 15
#  svlen:  15
#  keylen: 15
#  deslen: 15
#  orglen: 15
#]
