Error: legacy_blast.pl command not found

Question

[venura]

Hi,

I am trying to run the following command

legacy_blast.pl blastall -i test.fa -d StDB –p blastp –e 1e-10 –b 5 –v 5 –m 8 –o Sol.blast

but getting following error ;

legact_blast.pl: command not found

I am using ncbi-blast+ 2.2.25 . Can someone help me on this regard? Thank you!

[venura]

Hello venura!

We believe that this post does not fit the main topic of this site.

found a solution.

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[GenoMax]

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Answer 1

[ATpoint]

It is not in PATH. Please google what PATH is in Unix systems and how to add executables to it. Alternatively, it it not executable, so chmod +x your.pl might help.

[venura]

blast is already in the PATH and perl script is executable. Still I am getting the same error :(.

[GenoMax]

What happens if you just run legacy_blast.pl? That should print the help dialog to screen.

[venura]

Getting the same error . legacy_blast.pl command not found

[GenoMax]

Interesting. So something is not properly set up.

I see

$ legacy_blast.pl 
NAME
    legacy_blast.pl - Convert BLAST command line invocations from NCBI C
    toolkit's implementation to NCBI C++ toolkit's implementation. 

(truncated)

What does which legacy_blast.pl produce?

[venura]

No output. nothing at all:|

[GenoMax]

I suggest you check your $PATH and the location of where the bin directory is in the blast package. Reconcile those if needed. Otherwise use full path to legacy_blast.pl location and see if you can get the in-line help to show up.

[venura]

When I use the full path as you suggested, I get the help file.

When I echo, i get the following #path/home/venura/miniconda3/bin:/home/venura/miniconda3/condabin:/home/venura/bin:/home/venura/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games

[GenoMax]

That tells us that your blast bin directory is not in your $PATH. Add it by doing export PATH=$PATH:/full_path_to_blast_bin and you should be all set.

[venura]

Thank you! I know its not possible. But, I am darn sure that blast was there in the $PATH earlier :(.