package=biocat
  comment=BioCatalog of Software from EBI
  local_dir=/bio/archive/biosoft-catalog/
  local_ignore=([^Z]$|local$)
  recursive=false
  remote_dir=/pub/databases/bio_catal/
  site=ftp.ebi.ac.uk


package=blastdb
  comment=Blast DB from NCBI
  exclude_patt=(^month|^old)
  get_patt=(\.(gz|Z)$|README)
  local_dir=/bio/biomir-pub/biomirror/blast/
  local_ignore=(^month|local$)
  recursive=false
  remote_dir=/blast/db/
  site=ftp.ncbi.nih.gov


package=blastdbnew
  comment=Blast DB daily updates from NCBI
  get_patt=(^month.*\.(gz|Z)$)
  local_dir=/bio/biomir-pub/biomirror/blast/
  local_ignore=(^(?!month).*)
  recursive=false
  remote_dir=/blast/db/
  site=ftp.ncbi.nih.gov


package=blocks
  comment=BLOCKS from NCBI
  #exclude_patt=(^Old|\.tar$)
  #get_patt=(^blocks-11|^README)
  local_dir=/bio/biomir-pub/biomirror/blocks/data-blocks/
  #name_mappings=s|^blocks[^\/]*/||
  recursive=false
  remote_dir=/repository/blocks/unix/current/
  site=ftp.ncbi.nih.gov


package=blocksplus
  comment=BLOCKS Plus from NCBI
  exclude_patt=(^Old|\.tar$)
  get_patt=(^blocksplus)
  local_dir=/bio/biomir-pub/biomirror/blocks/blocksplus
  name_mappings=s|^blocksplus[^\/]*/||
  recursive=true
  remote_dir=/repository/blocks/unix/
  site=ftp.ncbi.nih.gov

package=celegans_ncbi
  comment=C. elegans AceDB data from NCBI
  get_patt=(^database.WS.*.tar\.(gz|Z)|README|INSTALL)
  local_dir=/bio/biomir-pub/biomirror/eugenes/celegans/
  recursive=false
  remote_dir=/repository/acedb/celegans/
  site=ftp.ncbi.nih.gov

package=celegans
  comment=C. elegans AceDB data from Sanger
  get_patt=(^database.WS.*.tar.(gz|Z)|wspec|CHROMOSOME|README|INSTALL)
  ##local_dir=/bio/biomir-pub/biomirror/eugenes/celegans/
  local_dir=/c6/tmp/worm/current_release/
  recursive=true
  remote_dir=/pub/wormbase/current_release/
  exclude_patt+pictures|additional_files|core|~$
  site=ftp.sanger.ac.uk

package=ddbj
  comment=DDBJ from AFFRC/bio-mirror
  exclude_patt=(\.Z|\.idx\.Z|ddbjgss\.seq\.Z|core)
  ##exclude_patt=(\.idx\.Z|ddbjgss\.seq\.Z|core)
  local_dir=/bio/biomir-pub/biomirror/ddbj/regular_release/
  recursive=false
  remote_dir=/pub/biomirror/ddbj/regular_release/
  site=bio-mirror.jp.apan.net


package=ddbjnew
  comment=DDBJ daily from AFFRC/bio-mirror
  exclude_patt=(core|DDBJNEWr46|DDBJNEWr40|DDBJNEWr35|DDBJNEWr36|DDBJNEWr37|DDBJNEWr38|DDBJNEWr39)
  local_dir=/bio/biomir-pub/biomirror/ddbj/daily_updates/
  max_delete_files=100%
  recursive=false
  remote_dir=/pub/biomirror/ddbj/daily_updates/
  site=bio-mirror.jp.apan.net


package=embl
  comment=EMBL from EBI
  local_dir=/bio/biomir-pub/biomirror/embl/release/
  recursive=false
  remote_dir=/pub/databases/embl/release/
  site=ftp.ebi.ac.uk
  compress_prog=gzip
  ## get all to be on ebi list of official mirrors
  #exclude_patt=(^gcg|^emvec|^Old)
  #get_patt=(\.dat\.gz$|^Release|README|\.doc$)


package=emblnew
  comment=EMBL daily from EBI
  exclude_patt=(^gcg|^list)
  #get_patt=(^cum_\S+\.dat\.gz$|README)
  #recursive=false
  exclude_patt=(week|gcg|old|cumulative)
  recursive=true
  local_dir=/bio/biomir-pub/biomirror/embl/new/
  max_delete_files=100%
  remote_dir=/pub/databases/embl/new/
  site=ftp.ebi.ac.uk
  mail_to=biomirror-trigger


package=enzyme
  comment=Enzyme from ExPASy
  local_dir=/bio/biomir-pub/biomirror/enzyme/
  remote_dir=/databases/enzyme/
  site=ca.expasy.org
## was expasy.hcuge.ch


package=fbgn
  comment=Drosophila Genes from FlyBase
	## FBgn.acode, FBgn.summary.acode
  ##get_patt=(FBgn.acode$)
  get_patt=(FBgn.*\.acode$)
  local_dir=/bio/biomir-pub/biomirror/eugenes/fly/
  local_ignore+\.i$|\.is$|local$
  recursive=false
  remote_dir=/data-archive/acode/data/
  remote_password=FlyBase
  remote_user=fbarchive
  site=flybase.net

# obsolete? - now getting all thru genbankall
package=gbgenomes
  comment=Genome section, Genbank from NCBI
  exclude_patt=(Old/|\%$)
  get_patt=(\.gbk|\.gbs|\.ptt|scaffold_map|dmrelease.txt|README$)
  local_dir=/bio/biomir-pub/biomirror/genbank/genomes/
  recursive=true
  remote_dir=/ncbi-genbank/genomes/
  site=ftp.ncbi.nih.gov


package=ncbigenomes
  comment=Genomes from NCBI
  local_dir=/bio/biomir-pub/biomirror/ncbigenomes/
  recursive=true
  remote_dir=/genomes/
  site=ftp.ncbi.nih.gov 
  compress_prog=gzip

package=genbank
  comment=GenBank from NCBI
  exclude_patt=(^genomes|^vms|^daily)
  #get_patt=(\.seq\.Z$|^gbrel\.txt|README|release\.notes)
  get_patt=(\.seq\.(gz|Z)$|^gbrel\.txt|README|release\.notes)
  local_dir=/bio/biomir-pub/biomirror/genbank/
  local_ignore=(^daily|^genomes|local$)
  recursive=false
  remote_dir=/ncbi-genbank/
  site=ftp.ncbi.nih.gov


package=genbankall
  comment=Full GenBank from NCBI
  local_dir=/bio/biomir-pub/biomirror/genbank/
  recursive=true
  remote_dir=/ncbi-genbank/
  site=ftp.ncbi.nih.gov
  mail_to=biomirror-trigger

package=genbanknew
  comment=GenBank daily nc updates from NCBI
  exclude_patt=(^Old)
  #get_patt=(^nc.+\.flat\.Z$|README)
  get_patt=(^nc.+\.flat\.(gz|Z)$|README)
  local_dir=/bio/biomir-pub/biomirror/genbank/daily-nc/
  max_delete_files=100%
  recursive=false
  remote_dir=/ncbi-genbank/daily-nc/
  site=ftp.ncbi.nih.gov
  mail_to=biomirror-trigger

package=genpept
  comment=GenPept from NCI
  get_patt=(^gpdat.+\.seq\.(gz|Z)$|^release|^announce|\.txt)
  local_dir=/bio/biomir-pub/biomirror/genpept/
  recursive=false
  remote_dir=/pub/genpept/
  site=ftp.ncifcrf.gov
  local_ignore=(^updates|local$)

package=genpeptnew
  comment=GenPept Cumulative Updates from NCI 
  get_patt=(^gpseq_updates\..+(gz|Z)$|\.header$|\.summary$)
  local_dir=/bio/biomir-pub/biomirror/genpept/updates/
  recursive=false
  remote_dir=/pub/genpept/updates/
  site=ftp.ncifcrf.gov
  mail_to=biomirror-trigger

package=interpro
  comment=InterPro Protein databank from EBI
  local_dir=/bio/biomir-pub/biomirror/interpro/
  remote_dir=/pub/databases/interpro/
  site=ftp.ebi.ac.uk


package=locuslink
  comment=LocusLink data from NCBI
  exclude_patt=(^Old)
  #get_patt=(LL_tmpl.(Z|gz)$|README)
  get_patt=(LL_tmpl|README)
  local_dir=/bio/biomir-pub/biomirror/eugenes/human/
  recursive=false
  remote_dir=/refseq/LocusLink/
  site=ftp.ncbi.nih.gov


package=mgd
  comment=Mouse Genome data from MGD
  get_patt=(GDB_Accession|MRK_Dump2|MRK_MLC|MRK_Sequence|MRK_SwissProt|index.html|tab-delimited.html)
  local_dir=/bio/biomir-pub/biomirror/eugenes/mouse/
  recursive=false
  remote_dir=/pub/informatics/reports/
  site=ftp.informatics.jax.org


package=pirncbi
  comment=PIR from NCBI
  get_patt=(\.dat\.(gz|Z)$|README)
  local_dir=/bio/biomir-pub/biomirror/pir/
  recursive=false
  remote_dir=/repository/PIR/ascii/
  site=ftp.ncbi.nih.gov

package=pir
  comment=PIR from NBRF, Georgetown
  local_dir=/bio/biomir-pub/biomirror/pir/release/
  site=nbrfa.georgetown.edu
  remote_dir=/pir_databases/psd/codata/
  ##remote_dir=/pir/databases/pir_codata/
  ##remote_dir=/pir/databases/
  recursive=false
  get_patt=(\.dat\.(gz|Z)$|README)
  ##get_patt=(pir_codata\/.+\.dat\.Z$|nrl_3d_codata\/.+\.dat\.Z$|README)

## pirnew is gone - nov01
package=pirnew
  comment=PIR updates from NBRF, Georgetown
  local_dir=/bio/biomir-pub/biomirror/pir/new/
  site=nbrfa.georgetown.edu
  remote_dir=/pir/databases/pir_updates/
  recursive=false
  get_patt=(\.dat\.(gz|Z)$|README)


package=nrl3d
  comment=NRL3D from NBRF, Georgetown
  local_dir=/bio/biomir-pub/biomirror/pir/
  site=nbrfa.georgetown.edu
  remote_dir=/pir/databases/nrl_3d_codata/
  #remote_dir=/pir/databases/
  recursive=false
  get_patt=(\.dat\.(gz|Z)$|README)
  ##get_patt=(pir_codata\/.+\.dat\.Z$|nrl_3d_codata\/.+\.dat\.Z$|README)

## need to add nrl3d fetch now, in above /pir/databases/nrl_3d_codata


package=pfam
  comment=Pfam from WUSTL
  exclude_patt=(^diff|prior.tar|press_release)
  local_dir=/bio/biomir-pub/biomirror/pfam/
  recursive=true
  remote_dir=/pub/eddy/Pfam/
  site=ftp.genetics.wustl.edu

#moved to ftp://ftp.genetics.wustl.edu/pub/eddy/pfam-7.0/

package=prints
  comment=PRINTS from NCBI
  exclude_patt=(^Old|\.tar$)
  get_patt=(^prints)
  local_dir=/bio/biomir-pub/biomirror/blocks/data-prints/
  name_mappings=s|^prints[^\/]*/||
  recursive=true
  remote_dir=/repository/blocks/unix/
  site=ftp.ncbi.nih.gov


package=prosite
  comment=Prosite from ExPASy
  local_dir=/bio/biomir-pub/biomirror/prosite/
  remote_dir=/databases/prosite/
  site=ca.expasy.org
## was expasy.hcuge.ch


package=rebase
  comment=Rebase from neb.com
  get_patt=(^allenz\.|^bairoch\.|^gcg\.|^README|^Readme|^REBASE.DOC|^NEWS\.)
  local_dir=/bio/biomir-pub/biomirror/rebase/
  name_mappings=s|\.[0-9]+||
  recursive=false
  remote_dir=/pub/rebase/
  site=vent.neb.com


package=refseq
  comment=RefSeq from NCBI
  exclude_patt=(^release|^daily|^LocusLink)
  get_patt=(rscu.gbff.(gz|Z)$|rscu.gnp.Z$|README)
  local_dir=/bio/biomir-pub/biomirror/refseq/
  local_ignore=(^genomes|local$)
  recursive=true
  remote_dir=/refseq/
  site=ftp.ncbi.nih.gov


package=ricecdna
  comment=Rice genome project cDNA from AFFRC
  exclude_patt=previous
  get_patt=(maff_rice.seq|maff_rice.fasta)
  local_dir=/bio/biomir-pub/biomirror/rice/cdna/
  recursive=false
  remote_dir=/pub/dna_maff/
  site=ftp.dna.affrc.go.jp


package=sgd
  comment=Saccharomyces genome data from SGD
  get_patt=(gene_registry/registry.genenames.tab|gene_registry/READ_ME|ORF_Descriptions/orf_descriptions.tab|ORF_Descriptions/README|ORF_Locations/ORF_chr.*\.txt|ORF_Locations/README)
  local_dir=/bio/biomir-pub/biomirror/eugenes/yeast/
  recursive=true
  remote_dir=/pub/yeast/
  site=genome-ftp.stanford.edu


package=databanks
  comment=SRS databank info from EBI
  local_dir=/bio/biomir-pub/biomirror/srs-databanks/
  remote_dir=/pub/databases/databanks/
  site=ftp.ebi.ac.uk


package=swissprot
  comment=SwissProt main data from ExPASy
  get_patt=(README|sprot.*\.dat\.(Z|gz)$|userman\.txt\.(gz|Z)|relnotes\.txt\.(gz|Z))
  local_dir=/bio/biomir-pub/biomirror/swissprot/
  local_ignore+Readme|update|new-seq.dat|log$
  recursive=false
  remote_dir=/databases/swiss-prot/release_compressed/
  site=ca.expasy.org
## was expasy.hcuge.ch


package=swissnew
  comment=SwissProt new data from ExPASy
  get_patt=(new_seq\.dat\.(gz|Z)$)
  local_dir=/bio/biomir-pub/biomirror/swissprot/updates/
  local_ignore+Readme|update|new-seq.dat|log$
  recursive=false
  remote_dir=/databases/swiss-prot/updates_compressed/
  site=ca.expasy.org
## was expasy.hcuge.ch


package=tair
  comment=Arabidopsis locus data from TAIR
  get_patt=(locus.tab$|locus_on_meinke.tab$|README)
  local_dir=/bio/biomir-pub/biomirror/eugenes/arabidopsis/tair/
  recursive=false
  remote_dir=/home/tair/Locus/
  remote_password=tairpub
  remote_user=tairpub
  site=ftp.arabidopsis.org


package=taxonomy
  comment=Taxonomy data from EBI
  local_dir=/bio/biomir-pub/biomirror/taxonomy/ebi/
  remote_dir=/pub/databases/taxonomy/
  site=ftp.ebi.ac.uk


package=taxonomy_ncbi
  comment=Taxonomy data from NCBI
  get_patt=(\.gz$|readme|README)
  local_dir=/bio/biomir-pub/biomirror/taxonomy/ncbi/
  recursive=true
  remote_dir=/pub/taxonomy/
  site=ftp.ncbi.nih.gov


package=trembl
  comment=TrEMBL from ExPASy
  exclude_patt+|fasta
  get_patt=(README|trembl.*\.dat\.(gz|Z)$)
  local_dir=/bio/biomir-pub/biomirror/trembl/
  local_ignore+Readme|update|log$
  recursive=false
  remote_dir=/pub/databases/sp_tr_nrdb/
  site=ftp.ebi.ac.uk


# update jul01 - moved from unigene to UniGene in jan01 !
# keeps .gz and .Z forms of all files
package=unigene
  comment=Unigene from NCBI
  exclude_patt+^Old|\~$
  get_patt=(README|\.info$|\.gz$)
  local_dir=/bio/biomir-pub/biomirror/unigene/
  recursive=false
  ##remote_dir=/repository/unigene/
  remote_dir=/repository/UniGene/
  site=ftp.ncbi.nih.gov


package=zfin
  comment=Zebrafish Genome data from ZFIN
  local_dir=/bio/biomir-pub/biomirror/eugenes/fish/
  exclude_patt+.\sav
  remote_dir=/pub/transfer/MEOW/
  site=zfish.uoregon.edu