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author Jan Kanis <jan.code@jankanis.nl>
date Thu, 23 Jul 2015 12:24:40 +0200
parents 0c2a03f9740b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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Jan Kanis <jan.code@jankanis.nl>
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1 #This is a sample file distributed with Galaxy that is used to define a
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Jan Kanis <jan.code@jankanis.nl>
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2 #list of nucleotide BLAST 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> <database_caption> <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
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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 #So, for example, if your database is nt and the path to your base name
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12 #is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry
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13 #would look like this:
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14 #
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15 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
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16 #
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17 #and your /depot/data2/galaxy/blastdb/nt directory would contain all of
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18 #your "base names" (e.g.):
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19 #
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20 #-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr
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21 #-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin
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22 #-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
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23 #...etc...
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24 #
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25 #Your blastdb.loc file should include an entry per line for each "base name"
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26 #you have stored. For example:
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27 #
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28 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
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29 #wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk
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30 #test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test
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31 #...etc...
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32 #
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33 #You can download the NCBI provided protein databases like NT from here:
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34 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/
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35 #
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36 #See also blastdb_p.loc which is for any protein BLAST database, and
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37 #blastdb_d.loc which is for any protein domains databases (like CDD).
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38
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39 EUginius_plasmid Euginius plasmid insert /opt/galaxy/blastdbs/EUginius_plasmid_insert Example Gene Bank http://example.com/example-genebank/{defline[0]}/