Re: [Biskit-general] database location
Brought to you by:
graik
From: Thomas E. <te...@gm...> - 2009-12-09 15:25:59
|
2009/12/9 Raik Gruenberg <rai...@cr...> > This is weird. What does your BLASTDB look like? Maybe there's something > stupid like a trailing / or missing / in the beginning? Well, I guess you > checked that already 10 times. > > Have you put your fastacmd executable into the $PATH? > > What about blastall, does it give you the same error? > > Greetings, > Raik > > I can't create synbolic or hard links designating the databases, that's bizarre. If you look at this tutorial and search for blastall or fastacmd usage you will see that the database directory is explicitly defined every time with -d argument ( e.g. *blastall -i key.fa -d $BLAST_DB/nr -p blastp -o result.out). http://biochem.uthscsa.edu/~hs_lab/frames/molgen/lblast.html Perhaps you could add a BLAST_DB variable into *.settings_Mod.cfg and modify the python scripts accordingly. I tried to do that myself but could find the point where fastacmd command was invoked. Apparently I needed to search more, but I bet it's piece of cake for you. regards, Thomas |