Question: problem running local blast after downloading on MacOSX
0
gravatar for gusmonksu
5.0 years ago by
gusmonksu0
gusmonksu0 wrote:

Am newish to linux but very familiar with BLAST and I need to use BLAST locally through command line on my MacOSX (Yosemite)

I downloaded the BLAST+ using ncbi-blast-2.2.18+.dmg installer and following instructions on NCBI website. It installed the files into usr/local/ncbi/blast/bin but when I try and run any of the blast programs (eg tblastn) I get the following error 

-bash: tblastn: command not found

I can only run it from within the usr/local/ncbi/blast/bin directory where the programs reside

I have (as far as I can tell) followed various instructions about setting the paths but still no luck. 

Any help greatly appreciated

blast • 2.8k views
ADD COMMENTlink modified 5.0 years ago by Neilfws48k • written 5.0 years ago by gusmonksu0
0
gravatar for Neilfws
5.0 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

In a terminal, type:

echo $PATH

and press Enter. If the output does not include usr/local/ncbi/blast/bin then your path is not set correctly.

If you have edited one of the "dotfiles" to set the path (e.g. .profile or .bashrc), you need to source the file or open a new terminal for the changes to take effect.

ADD COMMENTlink written 5.0 years ago by Neilfws48k

Thanks, when I type 

echo $PATH

it returned

”/Users/st*******ey/ncbi/blast/bin:??

so clearly a path problem. I followed the various instructions (including those on BLASTS own instrctions) to change the path by putting things in .bash_profile (.bashrc is empty)

however what should be in there to correct the path issue?

Thanks

ADD REPLYlink written 5.0 years ago by gusmonksu0

Ok I have sorted it -  I worked it out myself by trial and error.

Thanks for your help- it got me there.

 

ADD REPLYlink written 5.0 years ago by gusmonksu0
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