#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# $RCSfile: srsdb.i,v $
# $Revision: 1.142.2.18 $
# $Date: 2004/01/08 15:49:17 $
# $Author: hilbers $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$MySite=$Site:[name:unix
##################################################
# DATA ROOT VARIABLES
#
# These variables define common locations for the databases.
# Edit/add things to your liking - You can use them in the
# database location section below
#
# they are supposed to go into the variable attribute
# on $MySite
#
# $Application_Root is used as path, prepending the
# application name in most application definitions
# (fasta.i, blastp.i etc). If you apps are not in the
# normal search path, you can put a value in here,
# but don't forget a trailing '/'
##################################################
variables:{
'GCGdataRoot'"/data/gcg"
'dataRoot'"($Env:SRSROOT)/data"
'MatrixRoot'"/data/appl/wash-blast2/matrix/aa"
'Application_Root'""
'ApplResults'"."
'ApplIndex'"."
'gunzip''/usr/local/bin/gunzip -f '
'hmmPfamDataRoot'"($Env:SRSROOT)/data/pfam"
}
libs:{
#####################################################
#
# Location of the database flatfiles. Uncomment databases which
# have and specify the correct location of the database files.
#
#####################################################
# The major sequence databases
$LibLoc:[$EMBL_DB enabled:n
includeFiles:{"SRSDB:embl.i" "SRSDB:embl.it"}
]
$LibLoc:[$EMBLREL_DB enabled:n
includeFiles:{"SRSDB:embl.i" "SRSDB:emblrelease.it"}
dir:"$dataRoot/embl/"
offDir:"$dataRoot/embl_tmp/"
]
$LibLoc:[$EMBLNEW_DB enabled:n
includeFiles:{"SRSDB:embl.i" "SRSDB:emblnew.it"}
dir:"$dataRoot/emblnew/"
offDir:"$dataRoot/emblnew_tmp/"
]
$LibLoc:[lib:$EMBLCONT_DB enabled:n includeFiles:{
'SRSDB:embl.i' 'SRSDB:emblcontigs.it'
} dir:"$dataRoot/emblcontigs/"
offDir:"$dataRoot/emblcontigs_tmp/"
]
$LibLoc:[lib:$EMBLWGS_DB enabled:n includeFiles:{
'SRSDB:embl.i' 'SRSDB:emblwgs.it'
} dir:"$dataRoot/emblwgs/"
offDir:"$dataRoot/emblwgs_tmp/"
]
$LibLoc:[lib:$EMBLTPA_DB enabled:n includeFiles:{
'SRSDB:embl.i' 'SRSDB:embltpa.it'
} dir:"$dataRoot/embltpa/"
offDir:"$dataRoot/embltpa_tmp/"
]
$LibLoc:[$GENBANK_DB enabled:n
includeFiles:{"SRSDB:genbank.i" "SRSDB:genbank.it"}
]
$LibLoc:[$GENBANKREL_DB enabled:n
includeFiles:{"SRSDB:genbank.i" "SRSDB:genbankrelease.it"}
dir:"$dataRoot/genbank/"
offDir:"$dataRoot/genbank_tmp/"
]
$LibLoc:[$GENBANKNEW_DB enabled:n
includeFiles:{"SRSDB:genbank.i" "SRSDB:genbanknew.it"}
dir:"$dataRoot/genbanknew/"
offDir:"$dataRoot/genbanknew_tmp/"
]
$LibLoc:[$GBNEWFILES_DB enabled:n
includeFiles:{"SRSDB:gbnewfiles.i" "SRSDB:gbnewfiles.it"}
dir:"$dataRoot/genbanknew/"
offDir:"$dataRoot/genbanknew_tmp/"
]
$LibLoc:[lib:$GENBANKWGS_DB enabled:n includeFiles:{
'SRSDB:genbank.i' 'SRSDB:genbankwgs.it'
} dir:"$dataRoot/genbankwgs/"
offDir:"$dataRoot/genbankwgs_tmp/"
]
$LibLoc:[$REFSEQ_DB enabled:n
includeFiles:{"SRSDB:genbank.i" "SRSDB:refseq.it"}
]
$LibLoc:[lib:$REFSEQREL_DB enabled:n includeFiles:{
'SRSDB:genbank.i' 'SRSDB:refseqrelease.it'
}
dir:"$dataRoot/refseq/"
offDir:"$dataRoot/refseq_tmp/"
]
$LibLoc:[lib:$REFSEQNEW_DB enabled:n includeFiles:{
'SRSDB:genbank.i' 'SRSDB:refseqnew.it'
}
dir:"$dataRoot/refseqnew/"
offDir:"$dataRoot/refseqnew_tmp/"
]
$LibLoc:[$REFSEQFILES_DB enabled:n
includeFiles:{"SRSDB:gbnewfiles.i" "SRSDB:refseqfiles.it"}
dir:"$dataRoot/refseqnew/"
offDir:"$dataRoot/refseqnew_tmp/"
]
$LibLoc:[$REFSEQPFILES_DB enabled:n
includeFiles:{"SRSDB:gbnewfiles.i" "SRSDB:refseqpfiles.it"}
dir:"$dataRoot/refseqpnew/"
offDir:"$dataRoot/refseqpnew_tmp/"
]
$LibLoc:[$REFSEQP_DB enabled:n
includeFiles:{"SRSDB:genbank.i" "SRSDB:refseqp.it"}
]
$LibLoc:[lib:$REFSEQPREL_DB enabled:n includeFiles:{
'SRSDB:genbank.i' 'SRSDB:refseqprelease.it'}
dir:"$dataRoot/refseqp/"
offDir:"$dataRoot/refseqp_tmp/"
]
$LibLoc:[lib:$REFSEQPNEW_DB enabled:n includeFiles:{
'SRSDB:genbank.i' 'SRSDB:refseqpnew.it'}
dir:"$dataRoot/refseqpnew/"
offDir:"$dataRoot/refseqpnew_tmp/"
]
$LibLoc:[$SWALL_DB enabled:n
includeFiles:{"SRSDB:swissprot.i"}
]
$LibLoc:[$TREMBL_DB enabled:n
includeFiles:{"SRSDB:swissprot.i" "SRSDB:trembl.it"}
]
$LibLoc:[$SWISSPROT_DB enabled:n
includeFiles:{"SRSDB:swissprot.i" "SRSDB:swissprot.it"}
]
$LibLoc:[$SWISSPROTREL_DB enabled:n
includeFiles:{"SRSDB:swissprot.i" "SRSDB:swissprotrelease.it"}
dir:"$dataRoot/swissprot/"
offDir:"$dataRoot/swissprot_tmp/"
]
$LibLoc:[$SWISSNEW_DB enabled:n
includeFiles:{"SRSDB:swissprot.i" "SRSDB:swissnew.it"}
dir:"$dataRoot/swissnew/"
offDir:"$dataRoot/swissnew_tmp/"
]
$LibLoc:[$SPTREMBL_DB enabled:n
includeFiles:{"SRSDB:swissprot.i" "SRSDB:sptrembl.it"}
dir:"$dataRoot/sptrembl/"
offDir:"$dataRoot/sptrembl_tmp/"
]
$LibLoc:[$REMTREMBL_DB enabled:n
includeFiles:{"SRSDB:swissprot.i" "SRSDB:remtrembl.it"}
dir:"$dataRoot/remtrembl/"
offDir:"$dataRoot/remtrembl_tmp/"
]
$LibLoc:[$TREMBLNEW_DB enabled:n
includeFiles:{"SRSDB:swissprot.i" "SRSDB:tremblnew.it"}
dir:"$dataRoot/tremblnew/"
offDir:"$dataRoot/tremblnew_tmp/"
]
$LibLoc:[$IPI_DB enabled:n
includeFiles:{"SRSDB:ipi.i" "SRSDB:swissprot.i" "SRSDB:ipi.it"}
dir:"$dataRoot/ipi/"
offDir:"$dataRoot/ipi_tmp/"
]
$LibLoc:[$PIR_DB enabled:n
includeFiles:{"SRSDB:pir.i" "SRSDB:pir.it"}
dir:"$dataRoot/pir/"
offDir:"$dataRoot/pir_tmp/"
]
$LibLoc:[$GENPEPT_DB enabled:n
includeFiles:{"SRSDB:genpept.i" "SRSDB:genpept.it"}
]
$LibLoc:[$GENPEPTREL_DB enabled:n
includeFiles:{"SRSDB:genpept.i" "SRSDB:genpeptrelease.it"}
dir:"$dataRoot/genpept/"
offDir:"$dataRoot/genpept_tmp/"
]
$LibLoc:[$GENPEPTNEW_DB enabled:n
includeFiles:{"SRSDB:genpept.i" "SRSDB:genpeptnew.it"}
dir:"$dataRoot/genpeptnew/"
offDir:"$dataRoot/genpeptnew_tmp/"
]
$LibLoc:[$GPNEWFILES_DB enabled:n
includeFiles:{"SRSDB:gbnewfiles.i" "SRSDB:gpnewfiles.it"}
dir:"$dataRoot/genpeptnew/"
offDir:"$dataRoot/genpeptnew_tmp/"
]
# specialised sequence databases
# $LibLoc:[$OGLYC_DB enabled:n includeFiles:"SRSDB:.i" dir:"$dataRoot/data/oglyc/"]
$LibLoc:[$NRL3D_DB enabled:n
includeFiles:{"SRSDB:nrl3d.i" "SRSDB:pir.i" "SRSDB:nrl3d.it"}
dir:"$dataRoot/nrl/"
offDir:"$dataRoot/nrl_tmp/"
]
$LibLoc:[$NAGENESEQ_DB enabled:n
includeFiles:{"SRSDB:nageneseq.i" "SRSDB:aageneseq.i" "SRSDB:nageneseq.it"}
dir:"$dataRoot/geneseq/"
offDir:"$dataRoot/geneseq_tmp/"
]
$LibLoc:[$AAGENESEQ_DB enabled:n
includeFiles:{"SRSDB:aageneseq.i" "SRSDB:aageneseq.it"}
dir:"$dataRoot/geneseq/"
offDir:"$dataRoot/geneseq_tmp/"
]
$LibLoc:[$NAGENESEQTAR_DB enabled:n
includeFiles:{"SRSDB:nageneseq.i" "SRSDB:aageneseq.i" "SRSDB:nageneseqtar.it"}
dir:"$dataRoot/geneseq_tmp/"
offDir:"$dataRoot/geneseq_tmp/"
]
$LibLoc:[$AAGENESEQTAR_DB enabled:n
includeFiles:{"SRSDB:aageneseq.i" "SRSDB:aageneseqtar.it"}
dir:"$dataRoot/geneseq_tmp/"
offDir:"$dataRoot/geneseq_tmp/"
]
$LibLoc:[$IMGT_DB enabled:n
includeFiles:{"SRSDB:imgt.i" "SRSDB:embl.i" "SRSDB:imgt.it"}
dir:"$dataRoot/imgt/"
offDir:"$dataRoot/imgt_tmp/"
]
$LibLoc:[$ENSEMBL_DB enabled:n
includeFiles:{"SRSDB:ensembl.i" "SRSDB:ensembl.it"}
dir:"$dataRoot/ensembl/"
offDir:"$dataRoot/ensembl_tmp/"
]
# protein domains/patterns/alignments etc
$LibLoc:[$PROSITE_DB enabled:n
includeFiles:{"SRSDB:prosite.i" "SRSDB:prosite.it"}
dir:"$dataRoot/prosite/"
offDir:"$dataRoot/prosite_tmp/"
]
$LibLoc:[$PROSITEDOC_DB enabled:n
includeFiles:{"SRSDB:prositedoc.i" "SRSDB:prositedoc.it"}
dir:"$dataRoot/prosite/"
offDir:"$dataRoot/prosite_tmp/"
]
$LibLoc:[$PRINTS_DB enabled:n
includeFiles:{"SRSDB:prints.i" "SRSDB:prints.it"}
dir:"$dataRoot/prints/"
offDir:"$dataRoot/prints_tmp/"
]
$LibLoc:[$BLOCKS_DB enabled:n
includeFiles:{"SRSDB:blocks.i" "SRSDB:blocks.it"}
dir:"$dataRoot/blocks/"
offDir:"$dataRoot/blocks_tmp/"
]
$LibLoc:[$PRODOM_DB enabled:n
includeFiles:{"SRSDB:prodom.i" "SRSDB:prodom.it"}
dir:"$dataRoot/prodom/"
offDir:"$dataRoot/prodom_tmp/"
]
$LibLoc:[$DOMO_DB enabled:n
includeFiles:{"SRSDB:domo.i" "SRSDB:domo.it"}
dir:"$dataRoot/domo/"
offDir:"$dataRoot/domo_tmp/"
]
$LibLoc:[$PFAMA_DB enabled:n
includeFiles:{"SRSDB:pfam.i" "SRSDB:pfama.it"}
dir:"$dataRoot/pfam/"
offDir:"$dataRoot/pfam_tmp/"
]
$LibLoc:[$PFAMB_DB enabled:n
includeFiles:{"SRSDB:pfam.i" "SRSDB:pfamb.it"}
dir:"$dataRoot/pfam/"
offDir:"$dataRoot/pfam_tmp/"
]
$LibLoc:[$PFAMHMM_DB enabled:n
includeFiles:{"SRSDB:pfamhmm.i" "SRSDB:pfamhmm.it"}
dir:"$dataRoot/pfam/"
offDir:"$dataRoot/pfam_tmp/"
]
$LibLoc:[$PFAMSEED_DB enabled:n
includeFiles:{"SRSDB:pfamseed.i" "SRSDB:pfamseed.it"}
dir:"$dataRoot/pfam/"
offDir:"$dataRoot/pfam_tmp/"
]
$LibLoc:[$SWISSPFAM_DB enabled:n
includeFiles:{"SRSDB:swisspfam.i" "SRSDB:swisspfam.it"}
dir:"$dataRoot/pfam/"
offDir:"$dataRoot/pfam_tmp/"
]
# various stuff
$LibLoc:[$ENZYME_DB enabled:n
includeFiles:{"SRSDB:enzyme.i" "SRSDB:enzyme.it"}
dir:"$dataRoot/enzyme/"
offDir:"$dataRoot/enzyme_tmp/"
]
$LibLoc:[$REBASE_DB enabled:n
includeFiles:{"SRSDB:rebase.i" "SRSDB:rebase.it"}
dir:"$dataRoot/rebase/"
offDir:"$dataRoot/rebase_tmp/"
]
$LibLoc:[$REBCOMM_DB enabled:n
includeFiles:{"SRSDB:rebcomm.i" "SRSDB:rebcomm.it"}
dir:"$dataRoot/rebase/"
offDir:"$dataRoot/rebase_tmp/"
]
# $LibLoc:[$TACGDATA_DB enabled:n includeFiles:"SRSDB:.i" dir:"$dataRoot/rebase/"
# offDir:"$dataRoot/rebase_tmp/"
# restrictTo:$Dummy_user]
$LibLoc:[$GENETICCODE_DB enabled:n
includeFiles:{"SRSDB:geneticcode.i" "SRSDB:geneticcode.it"}
dir:"$dataRoot/geneticcode/"
]
$LibLoc:[$TAXONOMY_DB enabled:n
includeFiles:{"SRSDB:taxonomy.i" "SRSDB:taxonomy.it"}
dir:"$dataRoot/taxonomy/"
offDir:"$dataRoot/taxonomy_tmp/"
]
$LibLoc:[$EPD_DB enabled:n
includeFiles:{"SRSDB:epd.i" "SRSDB:epd.it"}
dir:"$dataRoot/epd/"
offDir:"$dataRoot/epd_tmp/"
]
# the transfac files
$LibLoc:[$TFSITE_DB enabled:n
includeFiles:{"SRSDB:tfsite.i" "SRSDB:tfsite.it"}
dir:"$dataRoot/transfac/"
]
$LibLoc:[$TFCELL_DB enabled:n
includeFiles:{"SRSDB:tfcell.i" "SRSDB:tfcell.it"}
dir:"$dataRoot/transfac/"
]
$LibLoc:[$TFFACTOR_DB enabled:n
includeFiles:{"SRSDB:tffactor.i" "SRSDB:tffactor.it"}
dir:"$dataRoot/transfac/"
]
$LibLoc:[$TFCLASS_DB enabled:n
includeFiles:{"SRSDB:tfclass.i" "SRSDB:tfclass.it"}
dir:"$dataRoot/transfac/"
]
$LibLoc:[$TFGENE_DB enabled:n
includeFiles:{"SRSDB:tfgene.i" "SRSDB:tfgene.it"}
dir:"$dataRoot/transfac/"
]
$LibLoc:[$TFMATRIX_DB enabled:n
includeFiles:{"SRSDB:tfmatrix.i" "SRSDB:tfmatrix.it"}
dir:"$dataRoot/transfac/"
]
# genetics, ests etc.
$LibLoc:[$LOCUSLINK_DB enabled:n
includeFiles:{"SRSDB:locuslink.i" "SRSDB:locuslink.it"}
dir:"$dataRoot/locuslink/"
offDir:"$dataRoot/locuslink_tmp/"
]
$LibLoc:[$OMIM_DB enabled:n
includeFiles:{"SRSDB:omim.i" "SRSDB:omim.it"}
dir:"$dataRoot/omim/"
offDir:"$dataRoot/omim_tmp/"
]
$LibLoc:[$UNIGENE_DB enabled:n
includeFiles:{"SRSDB:unigene.i" "SRSDB:unigene.it"}
dir:"$dataRoot/unigene/"
offDir:"$dataRoot/unigene_tmp/"
]
$LibLoc:[$UNISEQ_DB enabled:n
includeFiles:{"SRSDB:uniseq.i" "SRSDB:uniseq.it"}
dir:"$dataRoot/unigene/"
offDir:"$dataRoot/unigene_tmp/"
]
$LibLoc:[$UNIEST_DB enabled:n
includeFiles:{"SRSDB:uniest.i" "SRSDB:uniest.it"}
dir:"$dataRoot/unigene/"
offDir:"$dataRoot/unigene_tmp/"
]
$LibLoc:[$UNILIB_DB enabled:n
includeFiles:{"SRSDB:unilib.i" "SRSDB:unilib.it"}
dir:"$dataRoot/unilib/"
offDir:"$dataRoot/unilib_tmp/"
]
$LibLoc:[$DBEST_DB enabled:n
includeFiles:{"SRSDB:dbest.i" "SRSDB:dbest.it"}
dir:"$dataRoot/dbest/"
offDir:"$dataRoot/dbest_tmp/"
]
$LibLoc:[$DBSTS_DB enabled:n
includeFiles:{"SRSDB:dbsts.i" "SRSDB:dbsts.it"}
dir:"$dataRoot/dbsts/"
offDir:"$dataRoot/dbsts_tmp/"
]
$LibLoc:[$DBGSS_DB enabled:n
includeFiles:{"SRSDB:dbgss.i" "SRSDB:dbgss.it"}
dir:"$dataRoot/dbgss/"
offDir:"$dataRoot/dbgss_tmp/"
]
# radiation hybridization
$LibLoc:[$RHPANEL_DB enabled:n
includeFiles:{"SRSDB:rhpanel.i" "SRSDB:rhpanel.it"}
dir:"$dataRoot/rhdb/"
offDir:"$dataRoot/rhdb_tmp/"
]
$LibLoc:[$RHMAP_DB enabled:n
includeFiles:{"SRSDB:rhmap.i" "SRSDB:rhmap.it"}
dir:"$dataRoot/rhdb/"
offDir:"$dataRoot/rhdb_tmp/"
]
$LibLoc:[$RHEXP_DB enabled:n
includeFiles:{"SRSDB:rhexp.i" "SRSDB:rhexp.it"}
dir:"$dataRoot/rhdb/"
offDir:"$dataRoot/rhdb_tmp/"
]
$LibLoc:[$RHDB_DB enabled:n
includeFiles:{"SRSDB:rhdb.i" "SRSDB:rhdb.it"}
dir:"$dataRoot/rhdb/"
offDir:"$dataRoot/rhdb_tmp/"
]
# metabolic pathways
$LibLoc:[$LENZYME_DB enabled:n
includeFiles:{"SRSDB:lenzyme.i" "SRSDB:lenzyme.it"}
dir:"$dataRoot/lenzyme/"
offDir:"$dataRoot/lenzyme_tmp/"
]
$LibLoc:[$LCOMPOUND_DB enabled:n
includeFiles:{"SRSDB:lcompound.i" "SRSDB:lcompound.it"}
dir:"$dataRoot/lcompound/"
offDir:"$dataRoot/lcompound_tmp/"
]
$LibLoc:[$PATHWAYTAR_DB enabled:n
includeFiles:{"SRSDB:pathway.i" "SRSDB:pathwaytar.it"}
dir:"$dataRoot/pathway/"
offDir:"$dataRoot/pathway/"
]
$LibLoc:[$PATHWAY_DB enabled:n
includeFiles:{"SRSDB:pathway.i" "SRSDB:pathway.it"}
dir:"$dataRoot/pathway/"
offDir:"$dataRoot/pathway/"
]
# structural libs
$LibLoc:[$PDB_DB enabled:n
includeFiles:{"SRSDB:pdb.i" "SRSDB:pdb.it"}
dir:"$dataRoot/pdb/"
offDir:"$dataRoot/pdb/"
]
$LibLoc:[$PDBMODEL_DB enabled:n
includeFiles:{"SRSDB:pdb.i" "SRSDB:pdbmodel.it"}
dir:"$dataRoot/pdbmodel/"
offDir:"$dataRoot/pdbmodel/"
]
$LibLoc:[$DSSP_DB enabled:n
includeFiles:{"SRSDB:dssp.i" "SRSDB:dssp.it"}
dir:"$dataRoot/dssp/"
offDir:"$dataRoot/dssp/"
]
$LibLoc:[$HSSP_DB enabled:n
includeFiles:{"SRSDB:hssp.i" "SRSDB:hssp.it"}
dir:"$dataRoot/hssp/"
offDir:"$dataRoot/hssp/"
]
$LibLoc:[$FSSP_DB enabled:n
includeFiles:{"SRSDB:fssp.i" "SRSDB:fssp.it"}
dir:"$dataRoot/fssp/"
offDir:"$dataRoot/fssp/"
]
$LibLoc:[$PDBFINDER_DB enabled:n
includeFiles:{"SRSDB:pdbfinder.i" "SRSDB:pdbfinder.it"}
dir:"$dataRoot/pdbfinder/"
offDir:"$dataRoot/pdbfinder_tmp/"
]
# Web Log Analysis libs
$LibLoc:[$LOGUSE_DB enabled:n
includeFiles:"SRSROOT:logs/loguse.i"
dir:"$dataRoot/../logs/usage/"]
$LibLoc:[$LOGCOUNT_DB enabled:n
includeFiles:"SRSROOT:logs/logcount.i"
dir:"$dataRoot/../logs/usage/"]
# the blast tools
$LibLoc:[$BLASTP_DB enabled:n
includeFiles:{"SRSDB:blastp.i" "SRSDB:blastp.it"}
dir:"$ApplResults/" indexDir:"$ApplIndex/"
]
$LibLoc:[$BLASTX_DB enabled:n
includeFiles:{"SRSDB:blastp.i" "SRSDB:blastx.i" "SRSDB:blastx.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$BLASTN_DB enabled:n
includeFiles:{"SRSDB:blastp.i" "SRSDB:blastn.i" "SRSDB:blastn.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$TBLASTX_DB enabled:n
includeFiles:{"SRSDB:blastp.i" "SRSDB:tblastx.i" "SRSDB:tblastx.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$TBLASTN_DB enabled:n
includeFiles:{"SRSDB:blastp.i" "SRSDB:tblastn.i" "SRSDB:tblastn.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$PSIBLAST_DB enabled:n
includeFiles:{"SRSDB:blastp.i" "SRSDB:psiblast.i" "SRSDB:psiblast.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
# the fasta tools
$LibLoc:[$FASTA_DB enabled:n
includeFiles:{"SRSDB:fasta.i" "SRSDB:fasta.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$NFASTA_DB enabled:n
includeFiles:{"SRSDB:fasta.i" "SRSDB:nfasta.i" "SRSDB:nfasta.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$FASTX_DB enabled:n
includeFiles:{"SRSDB:fasta.i" "SRSDB:fastx.i" "SRSDB:fastx.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$FASTY_DB enabled:n
includeFiles:{"SRSDB:fasta.i" "SRSDB:fasty.i" "SRSDB:fasty.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$TFASTA_DB enabled:n
includeFiles:{"SRSDB:fasta.i" "SRSDB:tfasta.i" "SRSDB:tfasta.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$TFASTX_DB enabled:n
includeFiles:{"SRSDB:fasta.i" "SRSDB:tfastx.i" "SRSDB:tfastx.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$TFASTY_DB enabled:n
includeFiles:{"SRSDB:fasta.i" "SRSDB:tfasty.i" "SRSDB:tfasty.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$SSEARCH_DB enabled:n
includeFiles:{"SRSDB:fasta.i" "SRSDB:ssearch.i" "SRSDB:ssearch.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
# other tools
$LibLoc:[$CLUSTALW_DB enabled:n
includeFiles:{"SRSDB:clustalw.i"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$NCLUSTALW_DB enabled:n
includeFiles:{"SRSDB:clustalw.i" "SRSDB:nclustalw.i"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$PROSITESEARCH_DB enabled:n
includeFiles:{"SRSDB:prositesearch.i" "SRSDB:prositesearch.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$RESTRICTIONMAP_DB enabled:n
includeFiles:{"SRSDB:restrictionmap.i" "SRSDB:restrictionmap.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$HMMSEARCH_DB enabled:n
includeFiles:{"SRSDB:hmmsearch.i" "SRSDB:hmmsearch.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$HMMPFAM_DB enabled:n
includeFiles:{"SRSDB:hmmpfam.i" "SRSDB:hmmpfam.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$HMMBUILD_DB enabled:n
includeFiles:{"SRSDB:hmmbuild.i" "SRSDB:hmmbuild.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$PRINTSCAN_DB enabled:n
includeFiles:{"SRSDB:printscan.i"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$WF_DB enabled:n
includeFiles:{"SRSDB:workflow.i"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
# XML databases
$LibLoc:[$INTERPRO_DB enabled:n
includeFiles:{"SRSDB:interpro.i" "SRSDB:interpro.it"}
dir:"$dataRoot/interpro/"
offDir:"$dataRoot/interpro_tmp/"
]
$LibLoc:[$IPRMATCHES_DB enabled:n
includeFiles:{"SRSDB:iprmatches.i" "SRSDB:iprmatches.it" "SRSDB:interpro.i" }
dir:"$dataRoot/interpro/"
offDir:"$dataRoot/interpro_tmp/"
]
# Users can submit data to these two databases, to make them available
# to applications.
#
$LibLoc:[$USERDNA_DB enabled:n
includeFiles:{"SRSDB:userdna.i" "SRSDB:userdna.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
$LibLoc:[$USERPROTEIN_DB enabled:n
includeFiles:{"SRSDB:userprotein.i" "SRSDB:userprotein.it"}
dir:"$ApplResults/"
indexDir:"$ApplIndex/"
]
# srs documentation data
$LibLoc:[$SRSBOOKS_DB enabled:y
includeFiles:{"SRSDB:srsbooks.i"}
dir:"($Env:SRSWWW)/doc/"
]
$LibLoc:[$SRSERRDOC_DB enabled:y
includeFiles:{"SRSDB:srserrors.i"}
dir:"($Env:SRSETC)/"
]
$LibLoc:[$SRSERRCODES_DB enabled:y
includeFiles:{"SRSDB:srserrors.i"}
dir:"($Env:SRSETC)/"
]
$LibLoc:[$CLASSCOM_DB enabled:y
includeFiles:{"SRSDB:classcom.i"}
dir:"($Env:SRSWWW)/doc/man/"
]
}
]
##################################################################
## DATABANK INTERNAL IDENTIFIERS
##################################################################
$srsdb=$SrsDb:[
libIds:{
# main sequence libs
$LibId:[1 lib:$EMBLREL_DB]
$LibId:[2 lib:$EMBLNEW_DB]
$LibId:[40 lib:$EMBLCONT_DB]
$LibId:[41 lib:$EMBLWGS_DB]
$LibId:[42 lib:$EMBLTPA_DB]
$LibId:[5 lib:$EMBL_DB]
$LibId:[3 lib:$GENBANKREL_DB]
$LibId:[43 lib:$GENBANKWGS_DB]
$LibId:[4 lib:$GENBANKNEW_DB]
$LibId:[6 lib:$GENBANK_DB]
$LibId:[7 lib:$REFSEQ_DB]
$LibId:[61 lib:$REFSEQREL_DB]
$LibId:[62 lib:$REFSEQNEW_DB]
$LibId:[23 lib:$REFSEQP_DB]
$LibId:[63 lib:$REFSEQPREL_DB]
$LibId:[64 lib:$REFSEQPNEW_DB]
$LibId:[24 lib:$GBNEWFILES_DB]
$LibId:[25 lib:$REFSEQFILES_DB]
$LibId:[26 lib:$REFSEQPFILES_DB]
$LibId:[8 lib:$TREMBL_DB]
$LibId:[9 lib:$SWALL_DB]
$LibId:[10 lib:$SWISSPROTREL_DB]
$LibId:[11 lib:$SWISSPROT_DB]
$LibId:[12 lib:$SWISSNEW_DB]
$LibId:[13 lib:$PIR_DB]
$LibId:[14 lib:$SPTREMBL_DB]
$LibId:[15 lib:$REMTREMBL_DB]
$LibId:[16 lib:$TREMBLNEW_DB]
$LibId:[17 lib:$GENPEPTREL_DB]
$LibId:[18 lib:$GENPEPTNEW_DB]
$LibId:[20 lib:$GENPEPT_DB]
$LibId:[28 lib:$GPNEWFILES_DB]
$LibId:[21 lib:$IPI_DB]
$LibId:[22 lib:$ENSEMBL_DB]
# specialised sequence libs
$LibId:[31 lib:$NRL3D_DB]
$LibId:[32 lib:$IMGT_DB]
$LibId:[33 lib:$AAGENESEQ_DB]
$LibId:[34 lib:$NAGENESEQ_DB]
# $LibId:[35 lib:$OGLYC_DB]
$LibId:[36 lib:$AAGENESEQTAR_DB]
$LibId:[37 lib:$NAGENESEQTAR_DB]
# structure databases
$LibId:[51 lib:$PDB_DB]
$LibId:[53 lib:$DSSP_DB]
$LibId:[54 lib:$HSSP_DB]
$LibId:[56 lib:$FSSP_DB]
$LibId:[57 lib:$PDBFINDER_DB]
# $LibId:[58 lib:$PDBREPORT_DB]
$LibId:[60 lib:$PDBMODEL_DB]
# protein domains, alignments patterns etc
$LibId:[71 lib:$PROSITE_DB]
$LibId:[72 lib:$PROSITEDOC_DB]
$LibId:[73 lib:$BLOCKS_DB]
$LibId:[74 lib:$DOMO_DB]
$LibId:[75 lib:$PRINTS_DB]
$LibId:[76 lib:$PFAMA_DB]
$LibId:[77 lib:$PFAMB_DB]
$LibId:[78 lib:$SWISSPFAM_DB]
$LibId:[79 lib:$PFAMHMM_DB]
$LibId:[80 lib:$PFAMSEED_DB]
$LibId:[81 lib:$PRODOM_DB]
# various (seq related) info
$LibId:[101 lib:$TAXONOMY_DB]
$LibId:[102 lib:$GENETICCODE_DB]
$LibId:[103 lib:$ENZYME_DB]
$LibId:[104 lib:$REBASE_DB]
$LibId:[105 lib:$REBCOMM_DB]
$LibId:[106 lib:$EPD_DB]
# transfac libs
$LibId:[130 lib:$TFSITE_DB]
$LibId:[131 lib:$TFFACTOR_DB]
$LibId:[132 lib:$TFCELL_DB]
$LibId:[133 lib:$TFCLASS_DB]
$LibId:[134 lib:$TFMATRIX_DB]
$LibId:[135 lib:$TFGENE_DB]
# radiation hybridization
$LibId:[151 lib:$RHDB_DB]
$LibId:[152 lib:$RHEXP_DB]
$LibId:[153 lib:$RHMAP_DB]
$LibId:[154 lib:$RHPANEL_DB]
# ets, sts, gss etc
$LibId:[201 lib:$DBEST_DB]
$LibId:[202 lib:$DBSTS_DB]
$LibId:[203 lib:$DBGSS_DB]
$LibId:[211 lib:$UNIGENE_DB]
# $LibId:[212 lib:$RNUNIGENE_DB]
# $LibId:[213 lib:$MMUNIGENE_DB]
$LibId:[214 lib:$UNISEQ_DB]
# $LibId:[215 lib:$RNUNISEQ_DB]
# $LibId:[216 lib:$MMUNISEQ_DB]
$LibId:[217 lib:$UNIEST_DB]
# $LibId:[218 lib:$RNUNIEST_DB]
# $LibId:[219 lib:$MMUNIEST_DB]
$LibId:[220 lib:$UNILIB_DB]
# mutations
$LibId:[300 lib:$OMIM_DB]
$LibId:[311 lib:$LOCUSLINK_DB]
#metabolic pathways
$LibId:[501 lib:$PATHWAY_DB]
$LibId:[502 lib:$LENZYME_DB]
$LibId:[503 lib:$LCOMPOUND_DB]
$LibId:[505 lib:$PATHWAYTAR_DB]
#application results
$LibId:[1021 lib:$FASTA_DB]
$LibId:[1022 lib:$FASTX_DB]
$LibId:[1023 lib:$FASTY_DB]
# do not use LibId 1024 !
$LibId:[1025 lib:$TFASTA_DB]
$LibId:[1026 lib:$TFASTX_DB]
$LibId:[1027 lib:$TFASTY_DB]
$LibId:[1028 lib:$NFASTA_DB]
$LibId:[1029 lib:$SSEARCH_DB]
# $LibId:[1030 lib:$FASTS_DB]
$LibId:[1041 lib:$BLASTP_DB]
$LibId:[1042 lib:$BLASTN_DB]
$LibId:[1043 lib:$BLASTX_DB]
$LibId:[1044 lib:$TBLASTN_DB]
$LibId:[1045 lib:$TBLASTX_DB]
$LibId:[1046 lib:$PSIBLAST_DB]
$LibId:[1005 lib:$CLUSTALW_DB]
$LibId:[1006 lib:$NCLUSTALW_DB]
# $LibId:[1007 lib:$PPSEARCH_DB]
$LibId:[1008 lib:$PROSITESEARCH_DB]
$LibId:[1009 lib:$RESTRICTIONMAP_DB]
$LibId:[1010 lib:$HMMPFAM_DB]
$LibId:[1011 lib:$HMMSEARCH_DB]
$LibId:[1012 lib:$HMMBUILD_DB]
$LibId:[1040 lib:$PRINTSCAN_DB]
$LibId:[1039 lib:$WF_DB]
$LibId:[1051 lib:$INTERPRO_DB]
$LibId:[1052 lib:$IPRMATCHES_DB]
# Web Log Analysis
$LibId:[5500 lib:$LOGUSE_DB]
$LibId:[5501 lib:$LOGCOUNT_DB]
# srs docs and things
# $LibId:[2001 lib:$SRSFAQ_DB]
$LibId:[2006 lib:$SRSBOOKS_DB]
$LibId:[2007 lib:$CLASSCOM_DB]
$LibId:[2100 lib:$USERDNA_DB]
$LibId:[2101 lib:$USERPROTEIN_DB]
$LibId:[2402 lib:$SRSERRCODES_DB]
$LibId:[2403 lib:$SRSERRDOC_DB]
}
]