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comparison tool-data/tophat_fusion_blastdb.loc.sample @ 1:75845643f9dd

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Requirement fixes and fixed sample loc file."
author devteam@galaxyproject.org
date Mon, 27 Jan 2014 14:30:21 -0500
parents 70f710e91120
children
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0:70f710e91120 1:75845643f9dd
1 #This is a sample file distributed with Galaxy that is used to define a 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 2 #list of nucleotide BLAST databases for tophat-fusion-post, using fod columns tab separated
3 #(longer whitespace are TAB characters): 3 #(longer whitespace are TAB characters):
4 # 4 #
5 #<unique_id> <database_caption> <base_name_path> 5 #<unique_id> <dbkey> <name> <path>
6 # 6 #
7 #The captions typically contain spaces and might end with the build date. 7 # For example:
8 #It is important that the actual database name does not have a space in
9 #it, and that there are only two tabs on each line.
10 # 8 #
11 #So, for example, if your database is nt and the path to your base name 9 # hg19 hg19 hg19-blast /depot/data2/galaxy/hg19/blastdb/
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 # 10 #
33 #You can download the NCBI provided protein databases like NT from here: 11 #You can download the NCBI provided protein databases like NT from here:
34 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/ 12 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/
35 # 13 #
36 #See also blastdb_p.loc which is for any protein BLAST database, and
37 #blastdb_d.loc which is for any protein domains databases (like CDD).