Updating BLAST+ and PATH variable

Question

[A_heath]

Hi all,

I have BLAST+ version 2.11.0+ on my Linux computer and I would like to update this version to the latest (2.13.0+).

I downloaded successfully the newest version from the NCBI website.

However, after carefull reading of the manual, I'm still having trouble configuring this new version instead of the previous one..

When I type from anywhere in a terminal:

$ blastn -version
$ blastn: 2.11.0+

whereas when I go directly into the bin folder of what I've downloaded:

$ blastn -version
$ blastn: 2.13.0+

So, the issue is with the PATH variable. To try to solve it, I did:

$ export PATH=$PATH:$HOME/ncbi-blast-2.13.0+

but it still doesn't work with the new version..

I know I always have trouble with the PATH variable when I'm installing/updating software. So if you have an idea on how to solve that, I would really appreciate it!

Many thanks for your help,

Answer 1

[Dave Carlson]

You should prepend instead of appending the new directory to your PATH:

export PATH=$HOME/ncbi-blast-2.13.0+:$PATH

Now, when you run your blastn command, the shell will look in the 2.13.0 folder first.

[A_heath]

Thank you for your help!

However, I still have the same issue whenever I type:

blastn -h

or

blastn -version

It always show the previous version of BLAST..

[Dave Carlson]

Try taking a look at what exactly is in your PATH by doing the following:

echo $PATH

Also, are you sure that /ncbi-blast-2.13.0+ is actually the directory that contains your Blast executables? I would think that they would most likely be found in a bin subdirectory.

[A_heath]

Thank you very much for your help, I found the solution!

So, I ran the following command:

echo $PATH

and I localized the bin folder of the miniconda environment (where blast is located in my computer). Then, I copied the content of the bin subfolder of the newest version of blast and pasted it in the miniconda/bin folder to replace the existing old version. I don't know if that's the proper way to do it but it works now!

Thanks again for your help,

Have a nice day

[Dave Carlson]

I would definitely not recommend manually changing the executable programs in your miniconda bin subdirectory. The version of Blast that you're actually running will be different from the version that miniconda thinks you have installed. This could easily create confusing headaches down the road.

Instead I would recommend simply having conda update to the latest version. You should be able to do one of the following:

conda update blast

Or if that doesn't work then do:

conda install blast=2.13.0

[A_heath]

Indeed, a simple:

conda update blast

did the trick!

So thank you very much for your time and the precious help provided!