Question: External hard drive BLASTDB path not recognized
0
gravatar for Jenez
3.6 years ago by
Jenez520
Sweden
Jenez520 wrote:

Hi there!

Hopefully this does not stray too far away from the bioinformatical side of the site...

Question:

I'm saving my local blast databases on an external hard drive. When trying to run analysis against these databases, I'm constantly forced to give the absolute path as my database argument instead of simply the name of the database.

I know the issues lies in the exported BLASTDB environmental variable, however I can't for the life of me figure out how to structure the path!

Currently, it looks like this in my .bash_profile file:

export BLASTDB="/media/<username>/<Drive name>/<Subfolders>/external_blast_dbs"

This does not work however, as I keep getting an error that the database can not be found (states that it can't find the database relative to my current working directory...). Google searches never mention how to structure the path when it comes to external hard drives...

How the heck do you get it to recognize the database outside of my home directory?

Thank you in advance.

ADD COMMENTlink modified 12 months ago by RamRS24k • written 3.6 years ago by Jenez520
1

Did you make sure that there are no spaces in any of the names in that path? If there are then remove them (replace with an "_") and try. You could try and escape them but the former option is cleaner.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by genomax71k

No spaces present!

ADD REPLYlink written 3.6 years ago by Jenez520
1

I kind of feel like an idiot for asking, but have you sourced .bash_profile?

ADD REPLYlink modified 12 months ago by RamRS24k • written 3.6 years ago by cbio410

Then that makes me an even bigger idiot for not trying it yet. Alas, it did not fix it, but I think it not being sourced contributed to the issue... Now it's at least showing up in the path where it states it cannot find the database:

[/home/<username>/<subfolders>/:media/<username>/<Drive name>/<subfolders>/external_blast_dbs:]

Edit:

It works! I missed a / in the final try.

source .bash_profile and a correct path fixed the problem!

ADD REPLYlink modified 12 months ago by RamRS24k • written 3.6 years ago by Jenez520

That's great! Glad it worked out!

ADD REPLYlink written 3.6 years ago by cbio410

Post your comment as an answer and i'll mark it as the correct one for future viewers!

ADD REPLYlink written 3.6 years ago by Jenez520

Source your .bash_profile kids!

ADD REPLYlink modified 12 months ago by RamRS24k • written 3.6 years ago by Jenez520

You are brave to be using an external drive to hold your blast database. Hopefully the database is small (or you are using a thunderbolt drive) :-)

ADD REPLYlink written 3.6 years ago by genomax71k
2
gravatar for cbio
3.6 years ago by
cbio410
cbio410 wrote:

Try sourcing your .bash_profile.

cd
source .bash_profile
ADD COMMENTlink modified 12 months ago by RamRS24k • written 3.6 years ago by cbio410
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