Mercurial > repos > clifinder > clifinder
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 |
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date | Wed, 10 Apr 2024 10:24:17 +0000 |
parents | feecd33c8390 |
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rev | line source |
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14
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
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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"
pierre.pouchin
parents:
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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"
pierre.pouchin
parents:
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3 #(longer whitespace are TAB characters): |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
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4 # |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
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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"
pierre.pouchin
parents:
diff
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6 # |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
diff
changeset
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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"
pierre.pouchin
parents:
diff
changeset
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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"
pierre.pouchin
parents:
diff
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9 # |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
diff
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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"
pierre.pouchin
parents:
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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"
pierre.pouchin
parents:
diff
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12 #could look like this: |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
diff
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13 # |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
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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"
pierre.pouchin
parents:
diff
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15 # |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
diff
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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"
pierre.pouchin
parents:
diff
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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"
pierre.pouchin
parents:
diff
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18 # |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
diff
changeset
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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"
pierre.pouchin
parents:
diff
changeset
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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"
pierre.pouchin
parents:
diff
changeset
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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"
pierre.pouchin
parents:
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22 #...etc... |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
diff
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23 # |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
diff
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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"
pierre.pouchin
parents:
diff
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25 # |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
diff
changeset
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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"
pierre.pouchin
parents:
diff
changeset
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27 # |
feecd33c8390
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
pierre.pouchin
parents:
diff
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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"
pierre.pouchin
parents:
diff
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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"
pierre.pouchin
parents:
diff
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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"
pierre.pouchin
parents:
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31 # |