Mercurial > repos > devteam > ncbi_blast_plus

annotate tool-data/blastdb_p.loc.sample @ 18:577d9c12411a draft

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v0.1.06, now using BLAST+ 2.2.31
author peterjc
date Mon, 07 Sep 2015 04:44:24 -0400
parents c16c30e9ad5b
children
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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 BLAST databases, using three columns tab separated:
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3 #
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4 # <unique_id>{tab}<database_caption>{tab}<base_name_path>
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5 #
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6 # The captions typically contain spaces and might end with the build date.
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7 # It is important that the actual database name does not have a space in
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8 # it, and that there are only two tabs on each line.
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9 #
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10 # You can download the NCBI provided protein databases like NR from here:
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11 # ftp://ftp.ncbi.nlm.nih.gov/blast/db/
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12 #
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13 # For simplicity, many Galaxy servers are configured to offer just a live
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14 # version of each NCBI BLAST database (updated with the NCBI provided
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15 # Perl scripts or similar). In this case, we recommend using the case
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16 # sensistive base-name of the NCBI BLAST databases as the unique id.
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17 # Consistent naming is important for sharing workflows between Galaxy
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18 # servers.
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19 #
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20 # For example, consider the NCBI "non-redundant" protein BLAST database
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21 # where you have downloaded and decompressed the files under /data/blastdb/
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22 # meaning at the command line BLAST+ would be run with something like
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23 # which would look at the files /data/blastdb/nr.p*:
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24 #
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25 # $ blastp -db /data/blastdb/nr -query ...
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26 #
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27 # In this case use nr (lower case to match the NCBI file naming) as the
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28 # unique id in the first column of blastdb_p.loc, giving an entry like
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29 # this:
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30 #
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31 # nr{tab}NCBI non-redundant (nr){tab}/data/blastdb/nr
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32 #
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33 # Alternatively, rather than a "live" mirror of the NCBI databases which
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34 # are updated automatically, for full reproducibility the Galaxy Team
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35 # recommend saving date-stamped copies of the databases. In this case
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36 # your blastdb_p.loc file should include an entry per line for each
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37 # version you have stored. For example:
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38 #
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39 # nr_05Jun2010{tab}NCBI NR (non redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nr
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40 # nr_15Aug2010{tab}NCBI NR (non redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nr
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41 # ...etc...
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42 #
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43 # See also blastdb.loc which is for any nucleotide BLAST database, and
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44 # blastdb_d.loc which is for any protein domains databases (like CDD).