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Ncbi toolkit on biolinux 8

Hi guys,

I am trying to install a program that requires to specify the path for the NCBI toolkit. Unfortunately I am new to Biolinux and we just got a new system up and no one to help me.

Did anyone had the same issue in the past? I have looked at what seems all folders /usr/ bin ; /usr/bioinf etc and I can only find the ncbi blast folder or the data folder.

Any idea of the location?

Thank you so much in advance

F.

next-gen alignment blast biolinux
• 2,770 views • link
updated by Ram Ram • written by flacchy • flacchy

Are you referring to NCBI eUtils entrez direct utilities?

If so then substitute esearch in place of blastn in @Pierre's example below.

• 1 views • link
updated by Ram Ram • written by GenoMax GenoMax

Hi... I've found it using

dpkg -L ncbi-tools-x11

But I still cannot find the library path, have you experience this in the past?

• 1 views • link
updated by Ram Ram • written by flacchy • flacchy

Something like

find / -type f -perm -700 -name "blastn"
• 1 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Thanks , I have tried which with no luck. I am looking for the ncbi_tools library in order to install Vicuna

• 1 views • link
updated by Ram Ram • written by flacchy • flacchy

Hi,

Thanks for the advice but it didn't work. I have manage to find all the locations where to find the package but no idea of where the lib is installed still. I have also try to find the makefile for the ncbi-tools to see the path there but couldn't locate it.

• 0 views • link
updated by Ram Ram • written by flacchy • flacchy

1 answer

SOLVE IT!

Thanks to Tim Carr of eResearch UCT.

when configuring the Ncbi-tools remove the --with-dll flag
then make and make install run without errors

Hope this can help someone else

F.

• 0 views • link
updated by Ram Ram • written by flacchy • flacchy

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