Mercurial > repos > devteam > ncbi_blast_plus

annotate tool-data/blastdb_p.loc.sample @ 0:432ea9614cc9 draft

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Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
author peterjc
date Fri, 30 Jan 2015 08:27:28 -0500
parents
children 5e9d5e536b79
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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1 #This is a sample file distributed with Galaxy that is used to define a
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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2 #list of protein BLAST databases, using three columns tab separated
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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3 #(longer whitespace are TAB characters):
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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4 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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5 #<unique_id> <database_caption> <base_name_path>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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6 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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7 #The captions typically contain spaces and might end with the build date.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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8 #It is important that the actual database name does not have a space in
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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9 #it, and that there are only two tabs on each line.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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10 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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11 #So, for example, if your database is NR and the path to your base name
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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12 #is /data/blastdb/nr, then the blastdb_p.loc entry would look like this:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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13 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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14 #nr{tab}NCBI NR (non redundant){tab}/data/blastdb/nr
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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15 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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16 #and your /data/blastdb directory would contain all of the files associated
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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17 #with the database, /data/blastdb/nr.*.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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18 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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19 #Your blastdb_p.loc file should include an entry per line for each "base name"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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20 #you have stored. For example:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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21 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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22 #nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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23 #nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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24 #...etc...
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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25 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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26 #You can download the NCBI provided protein databases like NR from here:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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27 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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28 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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29 #See also blastdb.loc which is for any nucleotide BLAST database, and
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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30 #blastdb_d.loc which is for any protein domains databases (like CDD).