SCAFFOLD = [ fa http://www.bioinformatics.nl/wintermoth/data_files/Obru1.fsa.gz ]
  GFF = [ gff3 http://www.bioinformatics.nl/wintermoth/data_files/Obru_genes.gff.gz ]
  PROTEIN = [ fa http://www.bioinformatics.nl/wintermoth/data_files/ObruPep.fasta.gz ]

Each line in the [FILES] stanza assigns a space-separated array of values to a particular key, which can then be referenced elsewhere in the .ini file. Some key names are optional and/or arbitrary, while others, such as GFF and SCAFFOLD are referenced in the import scripts and must be specified with the expected file type.

  FILE = [ type remote_location local_name ]

Within the values array:

  • The first position specifies the file type and may be fa, agp, gff3 or txt.
  • The second position is the path to the file, and may be of the form http://example.com/filename, ftp://ftp.exampl.com/filename or /path/to/filename. Files will also be retrieved by scp from locations matching the pattern server:/path/to/filename in which case it is best to use ssh_config to manage login to the remote server.
  • The third position is optional and should be a local name to use for the downloaded file, which may be used to ensure files downloaded from different sources are named consistently.
  SCAFFOLD = [ fa http://www.bioinformatics.nl/wintermoth/data_files/Obru1.fsa.gz ]

Details of the sequence file(s) to be imported.

  • If a SCAFFOLD file of type fa is provided, then a CONTIG file is optional and vice versa.
  • SCAFFOLD data can also be imported from an agp file provided CONTIG sequences are provided.
  • If no CONTIG file is provided, contigs will be imputed from runs of N in the SCAFFOLD sequence
  BLASTP =  [ BLASTP  http://download.lepbase.org/current/blastp/Operophtera_brumata_v1_-_proteins.fa.blastp.uniprot_sprot.1e-10.gz ]
  IPRSCAN = [ IPRSCAN http://download.lepbase.org/current/interproscan/Operophtera_brumata_v1_-_proteins.fa.interproscan.gz ]
  REPEATMASKER = [ REPEATMASKER http://download.lepbase.org/current/repeats/Operophtera_brumata_v1_-_scaffolds.fa.out.gz ]

Specifiy the (remote) locations of BLASTP, IPRSCAN and REPEATMASKER files as appropriate.