Mercurial > repos > peterjc > fastq_paired_unpaired
comparison tool-data/blastdb_p.loc.sample @ 2:fae4084a0bc0 draft
Uploaded v0.0.20, preview 5
Cope if cElementTree is missing in BLAST XML to tabular script.
| author | peterjc |
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| date | Thu, 02 May 2013 11:20:43 -0400 |
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| 1:2feaef06d388 | 2:fae4084a0bc0 |
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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 #(longer whitespace are TAB characters): | |
| 4 # | |
| 5 #<unique_id> <database_caption> <base_name_path> | |
| 6 # | |
| 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. | |
| 10 # | |
| 11 #So, for example, if your database is NR and the path to your base name | |
| 12 #is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: | |
| 13 # | |
| 14 #nr{tab}NCBI NR (non redundant){tab}/data/blastdb/nr | |
| 15 # | |
| 16 #and your /data/blastdb directory would contain all of the files associated | |
| 17 #with the database, /data/blastdb/nr.*. | |
| 18 # | |
| 19 #Your blastdb_p.loc file should include an entry per line for each "base name" | |
| 20 #you have stored. For example: | |
| 21 # | |
| 22 #nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr | |
| 23 #nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr | |
| 24 #...etc... | |
| 25 # | |
| 26 #You can download the NCBI provided protein databases like NR from here: | |
| 27 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/ | |
| 28 # | |
| 29 #See also blastdb.loc which is for any nucleotide BLAST database, and | |
| 30 #blastdb_d.loc which is for any protein domains databases (like CDD). |