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comparison tool-data/blastdb_p.loc.sample @ 2:2f9619adab91 draft
planemo upload commit 76744a97a6f837ee60104321867e6451fec78d74-dirty
| author | iuc |
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| date | Sat, 05 Nov 2016 10:37:44 -0400 |
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| 1:b573ecb2ca66 | 2:2f9619adab91 |
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| 1 # This is a sample file distributed with Galaxy that is used to define a | |
| 2 # list of protein 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 "non-redundant" protein BLAST database | |
| 21 # where you have downloaded and decompressed the files under /data/blastdb/ | |
| 22 # meaning at the command line BLAST+ would be run with something like | |
| 23 # which would look at the files /data/blastdb/nr.p*: | |
| 24 # | |
| 25 # $ blastp -db /data/blastdb/nr -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 # nr{tab}NCBI non-redundant (nr){tab}/data/blastdb/nr | |
| 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_p.loc file should include an entry per line for each | |
| 37 # version you have stored. For example: | |
| 38 # | |
| 39 # nr_05Jun2010{tab}NCBI NR (non redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nr | |
| 40 # nr_15Aug2010{tab}NCBI NR (non redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nr | |
| 41 # ...etc... | |
| 42 # | |
| 43 # See also blastdb.loc which is for any nucleotide BLAST database, and | |
| 44 # blastdb_d.loc which is for any protein domains databases (like CDD). |