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annotate tools/ncbi_blast_plus/blastdb_p.loc.sample @ 2:45ba7c750bc8 draft

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This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
author peterjc
date Thu, 20 Sep 2012 10:12:43 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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1 #This is a sample file distributed with Galaxy that is used to define a
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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2 #list of protein BLAST databases, using three columns tab separated
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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3 #(longer whitespace are TAB characters):
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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4 #
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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5 #<unique_id> <database_caption> <base_name_path>
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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6 #
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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7 #The captions typically contain spaces and might end with the build date.
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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8 #It is important that the actual database name does not have a space in it,
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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9 #and that the first tab that appears in the line is right before the path.
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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10 #
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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11 #So, for example, if your database is NR and the path to your base name
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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12 #is /data/blastdb/nr, then the blastdb_p.loc entry would look like this:
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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13 #
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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14 #nr NCBI NR (non redundant) /data/blastdb/nr
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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15 #
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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16 #and your /data/blastdb directory would contain all of the files associated
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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17 #with the database, /data/blastdb/nr.*.
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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18 #
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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19 #Your blastdb_p.loc file should include an entry per line for each "base name"
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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20 #you have stored. For example:
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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21 #
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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22 #nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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23 #nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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24 #...etc...
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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25 #
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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26 #See also blastdb.loc which is for any nucleotide BLAST database.
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
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27 #