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annotate tool-data/blastdb_d.loc.sample @ 20:3034ce97dd33 draft

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Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
author peterjc
date Mon, 07 Nov 2016 11:31:37 -0500
parents c16c30e9ad5b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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1 # This is a sample file distributed with Galaxy that is used to define a
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2 # list of protein domain databases, using three columns tab separated
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3 # (longer whitespace are TAB characters):
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4 #
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5 # <unique_id>{tab}<database_caption>{tab}<base_name_path>
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6 #
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7 # The captions typically contain spaces and might end with the build date.
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8 # It is important that the actual database name does not have a space in
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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9 # it, and that there are only two tabs on each line.
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10 #
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11 # You can download the NCBI provided databases as tar-balls from here:
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12 # ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/
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13 #
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14 # For simplicity, many Galaxy servers are configured to offer just a live
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15 # version of each NCBI BLAST database (updated with the NCBI provided
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16 # Perl scripts or similar). In this case, we recommend using the case
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17 # sensistive base-name of the NCBI BLAST databases as the unique id.
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18 # Consistent naming is important for sharing workflows between Galaxy
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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19 # servers.
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20 #
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21 # For example, consider the NCBI Conserved Domains Database (CDD), where
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22 # you have downloaded and decompressed the files under the directory
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23 # /data/blastdb/domains/ meaning at the command line BLAST+ would be
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24 # run as follows any would look at the files /data/blastdb/domains/Cdd.*:
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25 #
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26 # $ rpsblast -db /data/blastdb/domains/Cdd -query ...
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27 #
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28 # In this case use Cdd (title case to match the NCBI file naming) as the
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29 # unique id in the first column of blastdb_d.loc, giving an entry like
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30 # this:
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31 #
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32 # Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/domains/Cdd
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33 #
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34 # Your blastdb_d.loc file should include an entry per line for each "base name"
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35 # you have stored. For example:
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36 #
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37 # Cdd{tab}NCBI CDD{tab}/data/blastdb/domains/Cdd
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38 # Kog{tab}KOG (eukaryotes){tab}/data/blastdb/domains/Kog
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39 # Cog{tab}COG (prokaryotes){tab}/data/blastdb/domains/Cog
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40 # Pfam{tab}Pfam-A{tab}/data/blastdb/domains/Pfam
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41 # Smart{tab}SMART{tab}/data/blastdb/domains/Smart
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42 # Tigr{tab}TIGR /data/blastdb/domains/Tigr
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43 # Prk{tab}Protein Clusters database{tab}/data/blastdb/domains/Prk
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44 # ...etc...
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45 #
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46 # Alternatively, rather than a "live" mirror of the NCBI databases which
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47 # are updated automatically, for full reproducibility the Galaxy Team
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48 # recommend saving date-stamped copies of the databases. In this case
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49 # your blastdb_d.loc file should include an entry per line for each
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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50 # version you have stored. For example:
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51 #
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52 # Cdd_05Jun2010{tab}NCBI CDD 05 Jun 2010{tab}/data/blastdb/domains/05Jun2010/Cdd
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53 # Cdd_15Aug2010{tab}NCBI CDD 15 Aug 2010{tab}/data/blastdb/domains/15Aug2010/Cdd
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54 # ...etc...
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55 #
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56 # See also blastdb.loc which is for any nucleotide BLAST database, and
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57 # blastdb_p.loc which is for any protein BLAST databases.