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