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comparison tool-data/blastdb.loc.sample @ 0:e6799e98c5fb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
author iuc
date Tue, 05 Apr 2022 12:11:08 +0000
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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 #
4 # <unique_id>{tab}<database_caption>{tab}<base_name_path>
5 #
6 # The captions typically contain spaces and might end with the build date.
7 # It is important that the actual database name does not have a space in
8 # it, and that there are only two tabs on each line.
9 #
10 # You can download the NCBI provided protein databases like NR from here:
11 # ftp://ftp.ncbi.nlm.nih.gov/blast/db/
12 #
13 # For simplicity, many Galaxy servers are configured to offer just a live
14 # version of each NCBI BLAST database (updated with the NCBI provided
15 # Perl scripts or similar). In this case, we recommend using the case
16 # sensistive base-name of the NCBI BLAST databases as the unique id.
17 # Consistent naming is important for sharing workflows between Galaxy
18 # servers.
19 #
20 # For example, consider the NCBI partially non-redundant nucleotide
21 # nt BLAST database, where you have downloaded and decompressed the
22 # files under /data/blastdb/ meaning at the command line BLAST+ would
23 # would look at the files /data/blastdb/nt.n* when run with:
24 #
25 # $ blastn -db /data/blastdb/nt -query ...
26 #
27 # In this case use nr (lower case to match the NCBI file naming) as the
28 # unique id in the first column of blastdb_p.loc, giving an entry like
29 # this:
30 #
31 # nt{tab}NCBI partially non-redundant (nt){tab}/data/blastdb/nt
32 #
33 # Alternatively, rather than a "live" mirror of the NCBI databases which
34 # are updated automatically, for full reproducibility the Galaxy Team
35 # recommend saving date-stamped copies of the databases. In this case
36 # your blastdb.loc file should include an entry per line for each
37 # version you have stored. For example:
38 #
39 # nt_05Jun2010{tab}NCBI nt (partially non-redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nt
40 # nt_15Aug2010{tab}NCBI nt (partially non-redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nt
41 # ...etc...
42 #
43 # See also blastdb_p.loc which is for any protein BLAST database, and
44 # blastdb_d.loc which is for any protein domains databases (like CDD).