Due to our not having Internet access on our analysis network, we try to mirror portions of NCBI that are used in our work. If this is a duplication of effort in terms of the offline_download scripts, maybe some of what we have could be used to build the databases internally.
I won't include the entire higher-level directory structure, but assuming all of the following are within a single ncbi folder and are using the structure of the ncbi ftp, here is our mirror layout as you requested:
genomes/refseq/*
genomes/genbank/*
genomes/Viruses/*
genbank/.seq.gz
pub/taxonomy/
blast/db/nt* and nr* and the v5 versions
refseq/release/plasmid/*
I can also add other sections of the ftp if needed, if it would facilitate an easier internal build.
Thanks for any help in getting this working.
Due to our not having Internet access on our analysis network, we try to mirror portions of NCBI that are used in our work. If this is a duplication of effort in terms of the offline_download scripts, maybe some of what we have could be used to build the databases internally.
I won't include the entire higher-level directory structure, but assuming all of the following are within a single ncbi folder and are using the structure of the ncbi ftp, here is our mirror layout as you requested:
genomes/refseq/*
genomes/genbank/*
genomes/Viruses/*
genbank/.seq.gz
pub/taxonomy/
blast/db/nt* and nr* and the v5 versions
refseq/release/plasmid/*
I can also add other sections of the ftp if needed, if it would facilitate an easier internal build.
Thanks for any help in getting this working.