Question: NCBI BLAST+ on local Galaxy and associated .loc file entries
2.0 years ago by
lp.vandergouw • 10
lp.vandergouw • 10 wrote:
I recently downloaded a local instance of galaxy and added the NCBI BLAST+ tool from the toolshed. Now I downloaded both the nt and the nr databases from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ but when installed, only the nr database shows up. The databases are intsalled as followed:
nt(tab)NCBI nt 01 Nov 2016(tab)/media/lucas/Verbatim_2TB/BLAST/nt/nt in blastdb.loc nr(tab)NCBI nr 01 Nov 2016(tab)/media/lucas/Verbatim_2TB/BLAST/nr/nr in blastdb_p.loc
Does anyone know how I can fix this?
Kind regards, Lucas van der Gouw
ADD COMMENT • link •modified 2.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.0 years ago by lp.vandergouw • 10
Few things to check:
If you still have trouble after that, run the command below, then post the results, along with the exact lines from the blastdb.loc for the target database and we can help with syntax.
The indexes are all uncompressed, are all called nt..* and the path given in the blastdb.loc file is the absolute path. The output of the command is as follows:
and here is the content of the bastdb.loc file:
note that I used the exact same syntax for the nr database in bastdb_p.loc (replaced nt with nr) and that works like a charm
What happens if you change the file permissions so that they are user, group, world readable/executable? Restart Galaxy after the change.
so for some reason my file won't change: neither via GUI nor via
the nr files have the same permissions as the nt files
I decided to try and get my taxonomic profiles some other way, so I downloaden MetaPhlAn2 from the toolshed. However, same as blastn, it can not find the database even after changing the .loc file to contain:
Lucas, isn't nt & nr both Nucleotides?
from the NCBI BLAST readme: