Mercurial > repos > devteam > ncbi_blast_plus
diff tool-data/blastdb_d.loc.sample @ 9:9dabbfd73c8a draft
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
Also includes other minor improvements.
| author | peterjc |
|---|---|
| date | Thu, 25 Apr 2013 09:38:37 -0400 |
| parents | |
| children | c16c30e9ad5b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/blastdb_d.loc.sample Thu Apr 25 09:38:37 2013 -0400 @@ -0,0 +1,35 @@ +#This is a sample file distributed with Galaxy that is used to define a +#list of protein domain databases, using three columns tab separated +#(longer whitespace are TAB characters): +# +#<unique_id> <database_caption> <base_name_path> +# +#The captions typically contain spaces and might end with the build date. +#It is important that the actual database name does not have a space in it, +#and that there are only two tabs on each line. +# +#You can download the NCBI provided databases as tar-balls from here: +#ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ +# +#So, for example, if your database is CDD and the path to your base name +#is /data/blastdb/Cdd, then the blastdb_d.loc entry would look like this: +# +#Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/Cdd +# +#and your /data/blastdb directory would contain all of the files associated +#with the database, /data/blastdb/Cdd.*. +# +#Your blastdb_d.loc file should include an entry per line for each "base name" +#you have stored. For example: +# +#Cdd NCBI CDD /data/blastdb/domains/Cdd +#Kog KOG (eukaryotes) /data/blastdb/domains/Kog +#Cog COG (prokaryotes) /data/blastdb/domains/Cog +#Pfam Pfam-A /data/blastdb/domains/Pfam +#Smart SMART /data/blastdb/domains/Smart +#Tigr TIGR /data/blastdb/domains/Tigr +#Prk Protein Clusters database /data/blastdb/domains/Prk +#...etc... +# +#See also blastdb.loc which is for any nucleotide BLAST database, and +#blastdb_p.loc which is for any protein BLAST databases.