Mercurial > repos > galaxyp > blast_plus_remote_blastp
comparison tool-data/blastdb_p.loc.sample @ 5:22a767177ac9 draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
author | galaxyp |
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date | Fri, 20 Jan 2017 16:00:56 -0500 |
parents | a7f1634cd624 |
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4:a51980bc0ffe | 5:22a767177ac9 |
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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). |