annotate tool-data/blastdb.loc.sample @ 22:e50f9ebde308 draft default tip

planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 7c372dde3a9a59818eeabce66742c9f448ba0307
author clifinder
date Wed, 10 Apr 2024 10:24:17 +0000
parents feecd33c8390
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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1 #This is a sample file distributed with Galaxy that is used to define a
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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2 #list of nucleotide BLAST databases, using three columns tab separated
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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3 #(longer whitespace are TAB characters):
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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4 #
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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5 #<unique_id> <database_caption> <base_name_path>
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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6 #
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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7 #The captions typically contain spaces and might end with the release date.
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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8 #It is important that the actual database name does not have a space in it.
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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9 #
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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10 #So, for example, if your database is nt and the path to your base name
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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11 #is /galaxy/data/blastdb/nt/DDmmmYYYY/nt, then the blastdb.loc entry
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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12 #could look like this:
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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13 #
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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14 #02dec2009 nt 02-Dec-2009 /galaxy/data/blastdb/nt/02dec2009/nt
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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15 #
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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16 #A /galaxy/data/blastdb/nt/02dec2009 directory would contain all of
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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17 #the "nt" blast indexes from ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt* (e.g.):
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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18 #
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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19 #-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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20 #-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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21 #-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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22 #...etc...
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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23 #
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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24 #The blastdb.loc file should include one entry per line for each database.
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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25 #
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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26 #See also blastdb_p.loc, used for protein BLAST database.
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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27 #
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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28 #Note that for backwards compatibility with workflows, the <unique_id> of
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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29 #an entry must be the path that was in the original loc file.
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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30 #The metadata <unique_id> is the value stored in workflows for "database".
feecd33c8390 "planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
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31 #