Mercurial > repos > devteam > ncbi_blast_plus

annotate tool-data/blastdb_d.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 domain databases, using three columns tab separated
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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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
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6 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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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 it,
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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9 #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
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10 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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11 #You can download the NCBI provided databases as tar-balls from here:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
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12 #ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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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 #So, for example, if your database is CDD 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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15 #is /data/blastdb/Cdd, then the blastdb_d.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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16 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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17 #Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/Cdd
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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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 #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
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20 #with the database, /data/blastdb/Cdd.*.
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 #Your blastdb_d.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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23 #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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24 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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25 #Cdd NCBI CDD /data/blastdb/domains/Cdd
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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26 #Kog KOG (eukaryotes) /data/blastdb/domains/Kog
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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27 #Cog COG (prokaryotes) /data/blastdb/domains/Cog
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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28 #Pfam Pfam-A /data/blastdb/domains/Pfam
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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29 #Smart SMART /data/blastdb/domains/Smart
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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30 #Tigr TIGR /data/blastdb/domains/Tigr
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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31 #Prk Protein Clusters database /data/blastdb/domains/Prk
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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32 #...etc...
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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33 #
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
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34 #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
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35 #blastdb_p.loc which is for any protein BLAST databases.