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comparison tool-data/blastdb_p.loc.sample @ 5:22a767177ac9 draft

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planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
author galaxyp
date Fri, 20 Jan 2017 16:00:56 -0500
parents a7f1634cd624
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comparison
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4:a51980bc0ffe 5:22a767177ac9
1 #NOTE: This file comes from the tool galaxyp/blast_plus_remote_blastp 1 #NOTE: This file comes from the tool galaxyp/blast_plus_remote_blastp
2 # This is a sample file distributed with Galaxy that is used to define a
3 # list of protein BLAST databases, using three columns tab separated:
2 # 4 #
3 #This is a sample file distributed with Galaxy that is used to define a 5 # <unique_id>{tab}<database_caption>{tab}<base_name_path>
4 #list of protein BLAST databases, using three columns tab separated
5 #(longer whitespace are TAB characters):
6 # 6 #
7 #<unique_id> <database_caption> <base_name_path> 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
9 # it, and that there are only two tabs on each line.
8 # 10 #
9 #The captions typically contain spaces and might end with the build date. 11 # You can download the NCBI provided protein databases like NR from here:
10 #It is important that the actual database name does not have a space in 12 # ftp://ftp.ncbi.nlm.nih.gov/blast/db/
11 #it, and that there are only two tabs on each line.
12 # 13 #
13 #So, for example, if your database is NR and the path to your base name 14 # For simplicity, many Galaxy servers are configured to offer just a live
14 #is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: 15 # version of each NCBI BLAST database (updated with the NCBI provided
16 # Perl scripts or similar). In this case, we recommend using the case
17 # sensistive base-name of the NCBI BLAST databases as the unique id.
18 # Consistent naming is important for sharing workflows between Galaxy
19 # servers.
15 # 20 #
16 #nr{tab}NCBI NR (non redundant){tab}/data/blastdb/nr 21 # For example, consider the NCBI "non-redundant" protein BLAST database
22 # where you have downloaded and decompressed the files under /data/blastdb/
23 # meaning at the command line BLAST+ would be run with something like
24 # which would look at the files /data/blastdb/nr.p*:
17 # 25 #
18 #and your /data/blastdb directory would contain all of the files associated 26 # $ blastp -db /data/blastdb/nr -query ...
19 #with the database, /data/blastdb/nr.*.
20 # 27 #
21 #Your blastdb_p.loc file should include an entry per line for each "base name" 28 # In this case use nr (lower case to match the NCBI file naming) as the
22 #you have stored. For example: 29 # unique id in the first column of blastdb_p.loc, giving an entry like
30 # this:
23 # 31 #
24 #nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr 32 # nr{tab}NCBI non-redundant (nr){tab}/data/blastdb/nr
25 #nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr
26 #...etc...
27 # 33 #
28 #You can download the NCBI provided protein databases like NR from here: 34 # Alternatively, rather than a "live" mirror of the NCBI databases which
29 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/ 35 # are updated automatically, for full reproducibility the Galaxy Team
36 # recommend saving date-stamped copies of the databases. In this case
37 # your blastdb_p.loc file should include an entry per line for each
38 # version you have stored. For example:
30 # 39 #
31 #See also blastdb.loc which is for any nucleotide BLAST database, and 40 # nr_05Jun2010{tab}NCBI NR (non redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nr
32 #blastdb_d.loc which is for any protein domains databases (like CDD). 41 # nr_15Aug2010{tab}NCBI NR (non redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nr
42 # ...etc...
43 #
44 # See also blastdb.loc which is for any nucleotide BLAST database, and
45 # blastdb_d.loc which is for any protein domains databases (like CDD).