[Bio-linux-list] locating ncbi-tools-x11 lib folder

[Tim Booth]

Hi Flavia,

Three weeks of struggle sounds immensely frustrating.  If I can't get
something to work within about ten minutes I get unhappy.

It looks like several people have chipped in suggestions but nobody
actually tried downloading Vicuna.  I did.  It does require NCBI toolkit
v7 or later and I can tell you that this is not pre-packaged for Ubuntu
or Bio-Linux.  There is only ncbi-tools6.  I tried building ncbi_cxx
from source and I run into problems like you did.  It's very big and
complex.  I suspect this may explain the lack of an Ubuntu package.

But before I look more deeply into those issues, I notice that the
Vicuna download provides a file:

executable/vicuna-omp.static.linux64

And in the same folder is a readme.txt that states the file is ready to
run on Linux 64-bit. So what happens if you try just using this?

Ie. - in the Vicuna PDF manual jump straight to section 3.2 4 (c) and
then in part (d) where it says to run ./bin/vicuna instead run ./executable/vicuna-
omp.static.linux64

Any joy?

Cheers,

TIM


On Tue, Feb 23, 2016, at 04:55 PM, Flavia Flaviani wrote:
> Hi everyone,
>
> It's been 3 weeks now since I've started trying to install a program
> without success on Biolinux. Before writing here I have tried to post
> for help on Biostar but without much luck... you can view it  here
> (https://www.biostars.org/p/177810/) and here
> (https://www.biostars.org/p/178055/[1]) so I have decided to try and
> ask the biolinux users community.
>
> The program I need to install is called Vicuna
> (http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna)
> and it requires ncbi-toolkit. To make it run we need to set the path
> for the ncbi-tool/lib  in the configuration file. Unfortunately I
> cannot locate it . I have locate the package but when I try
>>> find / -name 'ncbi-tools-x11'
> I am still not able to locate the lib for the ncbi tools. (I have
> tried all various commands and options but with no success).
>
> Did anyone had the same issue in the past? Could anyone help?
>
>
> Thank you so much in advance
>
> Flavia
>
> --
> Flavia Flaviani
>
> *PhD student* Department of Molecular and Cell Biology University of
> Cape Town, South Africa  In collaboration with The marine Biological
> Association of the UK (Plymouth, UK) flvfla001 at myuct.ac.za
> flafla at mba.ac.uk
>
> _________________________________________________
> Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/bio-linux-list


--
Of course I'm a technophobe; I program computers for a living!
 


Links:

  1. https://www.biostars.org/p/178055/#178060
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