view tool-data/blastdb.loc.sample @ 6:856b73016ba1 draft

v0.1.05 - Update citation information now GigaScience paper is out

# This is a sample file distributed with Galaxy that is used to define a
# list of nucleotide BLAST databases, using three columns tab separated:
#
# <unique_id>{tab}<database_caption>{tab}<base_name_path>
#
# The captions typically contain spaces and might end with the build date.
# It is important that the actual database name does not have a space in
# it, and that there are only two tabs on each line.
#
# You can download the NCBI provided protein databases like NR from here:
# ftp://ftp.ncbi.nlm.nih.gov/blast/db/
#
# For simplicity, many Galaxy servers are configured to offer just a live
# version of each NCBI BLAST database (updated with the NCBI provided
# Perl scripts or similar). In this case, we recommend using the case
# sensistive base-name of the NCBI BLAST databases as the unique id.
# Consistent naming is important for sharing workflows between Galaxy
# servers.
#
# For example, consider the NCBI partially non-redundant nucleotide 
# nt BLAST database, where you have downloaded and decompressed the
# files under /data/blastdb/ meaning at the command line BLAST+ would
# would look at the files /data/blastdb/nt.n* when run with:
#
# $ blastn -db /data/blastdb/nt -query ...
#
# In this case use nr (lower case to match the NCBI file naming) as the
# unique id in the first column of blastdb_p.loc, giving an entry like
# this:
#
# nt{tab}NCBI partially non-redundant (nt){tab}/data/blastdb/nt
#
# Alternatively, rather than a "live" mirror of the NCBI databases which
# are updated automatically, for full reproducibility the Galaxy Team
# recommend saving date-stamped copies of the databases. In this case
# your blastdb.loc file should include an entry per line for each
# version you have stored. For example:
#
# nt_05Jun2010{tab}NCBI nt (partially non-redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nt
# nt_15Aug2010{tab}NCBI nt (partially non-redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nt
# ...etc...
#
# See also blastdb_p.loc which is for any protein BLAST database, and
# blastdb_d.loc which is for any protein domains databases (like CDD).