[FILES] 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
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
- The second position is the path to the file, and may be of the form
/path/to/filename. Files will also be retrieved by scp from locations matching the pattern
server:/path/to/filenamein which case it is best to use
ssh_configto 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.
[FILES] SCAFFOLD = [ fa http://www.bioinformatics.nl/wintermoth/data_files/Obru1.fsa.gz ]
Details of the sequence file(s) to be imported.
- If a
SCAFFOLDfile of type
fais provided, then a
CONTIGfile is optional and vice versa.
SCAFFOLDdata can also be imported from an
CONTIGsequences are provided.
- If no
CONTIGfile is provided, contigs will be imputed from runs of
[FILES] 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
REPEATMASKER files as appropriate.
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