Mercurial > repos > blankenberg > data_manager_example_blastdb_ncbi_update_blastdb
comparison tool-data/blastdb.loc.sample @ 0:c88d28377bd1 default tip
Create an example blastdb Data Manager.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
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| date | Wed, 11 Dec 2013 16:24:11 -0500 |
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| -1:000000000000 | 0:c88d28377bd1 |
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| 1 #This is a sample file distributed with Galaxy that is used to define a | |
| 2 #list of nucleotide BLAST databases, using three columns tab separated | |
| 3 #(longer whitespace are TAB characters): | |
| 4 # | |
| 5 #<unique_id> <database_caption> <base_name_path> | |
| 6 # | |
| 7 #The captions typically contain spaces and might end with the build date. | |
| 8 #It is important that the actual database name does not have a space in it, | |
| 9 #and that the first tab that appears in the line is right before the path. | |
| 10 # | |
| 11 #So, for example, if your database is nt and the path to your base name | |
| 12 #is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry | |
| 13 #would look like this: | |
| 14 # | |
| 15 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk | |
| 16 # | |
| 17 #and your /depot/data2/galaxy/blastdb/nt directory would contain all of | |
| 18 #your "base names" (e.g.): | |
| 19 # | |
| 20 #-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr | |
| 21 #-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin | |
| 22 #-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq | |
| 23 #...etc... | |
| 24 # | |
| 25 #Your blastdb.loc file should include an entry per line for each "base name" | |
| 26 #you have stored. For example: | |
| 27 # | |
| 28 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk | |
| 29 #wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk | |
| 30 #test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test | |
| 31 #...etc... | |
| 32 # | |
| 33 #See also blastdb_p.loc which is for any protein BLAST database. | |
| 34 # | |
| 35 #Note that for backwards compatibility with workflows, the unique ID of | |
| 36 #an entry must be the path that was in the original loc file, because that | |
| 37 #is the value stored in the workflow for that parameter. | |
| 38 # |