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peterjc
58 lines
2.6 KiB
Plaintext
58 lines
2.6 KiB
Plaintext
# This is a sample file distributed with Galaxy that is used to define a
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# list of protein domain databases, using three columns tab separated
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# (longer whitespace are TAB characters):
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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 databases as tar-balls from here:
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# ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/
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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 Conserved Domains Database (CDD), where
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# you have downloaded and decompressed the files under the directory
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# /data/blastdb/domains/ meaning at the command line BLAST+ would be
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# run as follows any would look at the files /data/blastdb/domains/Cdd.*:
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#
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# $ rpsblast -db /data/blastdb/domains/Cdd -query ...
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#
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# In this case use Cdd (title case to match the NCBI file naming) as the
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# unique id in the first column of blastdb_d.loc, giving an entry like
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# this:
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#
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# Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/domains/Cdd
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#
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# Your blastdb_d.loc file should include an entry per line for each "base name"
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# you have stored. For example:
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#
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# Cdd{tab}NCBI CDD{tab}/data/blastdb/domains/Cdd
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# Kog{tab}KOG (eukaryotes){tab}/data/blastdb/domains/Kog
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# Cog{tab}COG (prokaryotes){tab}/data/blastdb/domains/Cog
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# Pfam{tab}Pfam-A{tab}/data/blastdb/domains/Pfam
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# Smart{tab}SMART{tab}/data/blastdb/domains/Smart
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# Tigr{tab}TIGR /data/blastdb/domains/Tigr
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# Prk{tab}Protein Clusters database{tab}/data/blastdb/domains/Prk
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# ...etc...
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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_d.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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# Cdd_05Jun2010{tab}NCBI CDD 05 Jun 2010{tab}/data/blastdb/domains/05Jun2010/Cdd
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# Cdd_15Aug2010{tab}NCBI CDD 15 Aug 2010{tab}/data/blastdb/domains/15Aug2010/Cdd
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# ...etc...
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#
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# See also blastdb.loc which is for any nucleotide BLAST database, and
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# blastdb_p.loc which is for any protein BLAST databases.
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