MAKER installation problem: External Programs

Question

[yerspestis]

Please tell how to point the path to prerequisites. I tried to set the environment variable, but apparently did not cope with this (or what should I do here)

==============================================================================
STATUS MAKER v2.31.10
==============================================================================
PERL Dependencies:  VERIFIED
External Programs:  MISSING
          !  RepeatMasker
          !  BLAST
          !  Exonerate

[lieven.sterck]

Can we assume you went through the installation docs of MAKER?

[yerspestis]

Yes, but still not clear

[lieven.sterck]

OK, just making sure ;-)

[GenoMax]

Which environmental variable did you set?

[yerspestis]

From instruction:

Add the location where you installed NCBI-BLAST to your PATH variable in .bash_profile (i.e. PATH="/usr/local/ncbi-blast:$PATH").

---

I did it this way

nano ~/.bash_profile
export PATH="$PATH:/home/.../ncbi-blast-2.9.0+-x64-linux/ncbi-blast-2.9.0+'"
source ~/.bash_profile

[lieven.sterck]

Is that bash_profile file loaded by default? For instance in my linux environment it's the .bashrc file that is loaded (and where I have to put stuff like this)

Doing it the way you describe might not ensure that the PATH variable is also available to MAKER.

The path to your blast is correct? Can you now just type blastp for instance on the commandline?

[jean.elbers]

If you are having trouble with the installation, I haven't personally tried it, but perhaps you might give the bioconda recipe for MAKER a try. https://bioconda.github.io/recipes/maker/README.html