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

[Flavia Flaviani]

Hi Tim and Tony,

thought this might be of help for someone else that need to install the
NCBI-tools++,

while running the ./config for the tools, Tim Carr from eReseach at UCT
advice me to remove the --with-dll flag  (installing the libraries
statically instead of dynamic) and that solve the errors when running make.

Regards

Flavia


2016-02-24 0:25 GMT+00:00 Tim Booth <avarus at fastmail.fm>:

> 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/
> <https://www.biostars.org/p/178055/#178060>) 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!
>
>
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>


-- 
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
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