From flacchy at gmail.com  Wed Mar  2 10:38:25 2016
From: flacchy at gmail.com (Flavia Flaviani)
Date: Wed, 2 Mar 2016 15:38:25 +0000
Subject: [Bio-linux-list] locating ncbi-tools-x11 lib folder
In-Reply-To: <1456273523.681889.530002330.7C481840@webmail.messagingengine.com>
References: <CAAzKT9pJwiaSdMLx2Qmudu3SLH-Sy6VQS8t62mMAg5DRq-z8jg@mail.gmail.com>
	<1456273523.681889.530002330.7C481840@webmail.messagingengine.com>
Message-ID: <CAAzKT9oVigYEoyGLKV=xQei27dU4P1w-nwirz-0c=7Daow3L=w@mail.gmail.com>

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!
>
>
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/bio-linux-list
>
>


-- 
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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From tony.travis at minke-informatics.co.uk  Wed Mar  2 11:23:20 2016
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Wed, 2 Mar 2016 16:23:20 +0000
Subject: [Bio-linux-list] locating ncbi-tools-x11 lib folder
In-Reply-To: <CAAzKT9oVigYEoyGLKV=xQei27dU4P1w-nwirz-0c=7Daow3L=w@mail.gmail.com>
References: <CAAzKT9pJwiaSdMLx2Qmudu3SLH-Sy6VQS8t62mMAg5DRq-z8jg@mail.gmail.com>
	<1456273523.681889.530002330.7C481840@webmail.messagingengine.com>
	<CAAzKT9oVigYEoyGLKV=xQei27dU4P1w-nwirz-0c=7Daow3L=w@mail.gmail.com>
Message-ID: <56D71378.3000404@minke-informatics.co.uk>

On 02/03/16 15:38, Flavia Flaviani wrote:
> 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. 

Hi, Flavia.

Did you try the statically-linked binary provided as Tim suggested?

  VICUNA_v1.3/executable/vicuna-omp.static.linux64

Bye,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk

From paumarc at gmail.com  Wed Mar 30 07:22:50 2016
From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=)
Date: Wed, 30 Mar 2016 13:22:50 +0200
Subject: [Bio-linux-list] problem with the pakages
Message-ID: <CADFuJLi=ocAXmNbgJTTu2OkQkZAWeA-xBjzBvumBCWRYmcqVYw@mail.gmail.com>

Hi people

 I am having some problems with the packages, each time I do an apt-get
update I am having the following errors

W: Duplicate sources.list entry
http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main amd64 Packages
(/var/lib/apt/lists/ppa.launchpad.net_nebc_bio-linux_ubuntu_dists_trusty_main_binary-amd64_Packages)
W: Duplicate sources.list entry
http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main i386 Packages
(/var/lib/apt/lists/ppa.launchpad.net_nebc_bio-linux_ubuntu_dists_trusty_main_binary-i386_Packages)

what can i do?

Thanks

Pau Marc Mu?oz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
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From tony.travis at abdn.ac.uk  Wed Mar 30 09:35:03 2016
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Wed, 30 Mar 2016 14:35:03 +0100
Subject: [Bio-linux-list] problem with the pakages
In-Reply-To: <CADFuJLi=ocAXmNbgJTTu2OkQkZAWeA-xBjzBvumBCWRYmcqVYw@mail.gmail.com>
References: <CADFuJLi=ocAXmNbgJTTu2OkQkZAWeA-xBjzBvumBCWRYmcqVYw@mail.gmail.com>
Message-ID: <56FBD607.3020800@abdn.ac.uk>

On 30/03/16 12:22, Pau Marc Mu?oz Torres wrote:
> Hi people
>
>  I am having some problems with the packages, each time I do an apt-get
> update I am having the following errors
>
> W: Duplicate sources.list entry
> http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main amd64
> Packages
> (/var/lib/apt/lists/ppa.launchpad.net_nebc_bio-linux_ubuntu_dists_trusty_main_binary-amd64_Packages)
> W: Duplicate sources.list entry
> http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main i386
> Packages
> (/var/lib/apt/lists/ppa.launchpad.net_nebc_bio-linux_ubuntu_dists_trusty_main_binary-i386_Packages)
>
> what can i do?

Hi, Pau.

You need to check your sources.list files - This is what it should be:

> grep bio-linux /etc/apt/sources.list.d/*.list
> /etc/apt/sources.list.d/bio-linux-legacy.list:# deb http://distro.ibiblio.org/bio-linux/packages/ unstable bio-linux
> /etc/apt/sources.list.d/bio-linux-legacy.list:deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux
> /etc/apt/sources.list.d/nebc-bio-linux-trusty.list:deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main
> /etc/apt/sources.list.d/nebc-bio-linux-trusty.list:deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main

You might have some redundant *.list files if you've upgraded Bio-Linux
or have added other package source files e.g. the "cloudbio-linux.list".

HTH,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.

From paumarc at gmail.com  Thu Mar 31 05:23:17 2016
From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=)
Date: Thu, 31 Mar 2016 11:23:17 +0200
Subject: [Bio-linux-list] problem with the pakages
In-Reply-To: <56FBD607.3020800@abdn.ac.uk>
References: <CADFuJLi=ocAXmNbgJTTu2OkQkZAWeA-xBjzBvumBCWRYmcqVYw@mail.gmail.com>
	<56FBD607.3020800@abdn.ac.uk>
Message-ID: <CADFuJLgz7oh92CstMip51=JaEPO994nRZ4C18iQzYFxDKHYvPw@mail.gmail.com>

Thanks Tony

p

Pau Marc Mu?oz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/


2016-03-30 15:35 GMT+02:00 Tony Travis <tony.travis at abdn.ac.uk>:

> On 30/03/16 12:22, Pau Marc Mu?oz Torres wrote:
> > Hi people
> >
> >  I am having some problems with the packages, each time I do an apt-get
> > update I am having the following errors
> >
> > W: Duplicate sources.list entry
> > http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main amd64
> > Packages
> >
> (/var/lib/apt/lists/ppa.launchpad.net_nebc_bio-linux_ubuntu_dists_trusty_main_binary-amd64_Packages)
> > W: Duplicate sources.list entry
> > http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main i386
> > Packages
> >
> (/var/lib/apt/lists/ppa.launchpad.net_nebc_bio-linux_ubuntu_dists_trusty_main_binary-i386_Packages)
> >
> > what can i do?
>
> Hi, Pau.
>
> You need to check your sources.list files - This is what it should be:
>
> > grep bio-linux /etc/apt/sources.list.d/*.list
> > /etc/apt/sources.list.d/bio-linux-legacy.list:# deb
> http://distro.ibiblio.org/bio-linux/packages/ unstable bio-linux
> > /etc/apt/sources.list.d/bio-linux-legacy.list:deb
> http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux
> > /etc/apt/sources.list.d/nebc-bio-linux-trusty.list:deb
> http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main
> > /etc/apt/sources.list.d/nebc-bio-linux-trusty.list:deb-src
> http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main
>
> You might have some redundant *.list files if you've upgraded Bio-Linux
> or have added other package source files e.g. the "cloudbio-linux.list".
>
> HTH,
>
>   Tony.
>
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
>
>
> The University of Aberdeen is a charity registered in Scotland, No
> SC013683.
> Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir.
> SC013683.
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/bio-linux-list
>
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