[Bio-linux-list] locating ncbi-tools-x11 lib folder
Flavia Flaviani
flacchy at gmail.com
Wed Feb 24 04:54:09 EST 2016
Hi Tony,
thanks for helping, again.
I've checked and the package is installed:
% dpkg -l ncbi-tools-x11
Desired=Unknown/Install/Remove/Purge/Hold
|
Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name Version Architecture
Description
+++-=========================-=================-=================-========================================================
ii ncbi-tools-x11 6.1.20120620-7 amd64 NCBI
libraries for biology applications (X-based util
Then I've run the step after sudo -i that you suggested and got this:
root at biolinux:~# apt-file search ncbi-tools-x11
app-install-data:
/usr/share/app-install/desktop/ncbi-tools-x11:Cn3D-3.0.desktop
app-install-data:
/usr/share/app-install/desktop/ncbi-tools-x11:Psequin.desktop
app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:ddv.desktop
app-install-data:
/usr/share/app-install/desktop/ncbi-tools-x11:entrez2.desktop
app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:udv.desktop
med-bio: /usr/share/blends/med/menu/ncbi-tools-x11
ncbi-tools-x11: /usr/lib/mime/packages/ncbi-tools-x11
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.gz
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.sequin.gz
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/changelog.Debian.gz
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/copyright
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firedialog.gif
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firewall.html
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/affil.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/annot.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/authors.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/cds_edit.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/contact.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/desktop.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/format.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/genbank.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/graphic.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/loc_page.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/logo.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/ncbi_sequin.css
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/net_cfg.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucaln.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucset.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing1.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing2.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/organism.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/props_pg.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein1.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein2.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/sequence.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/submit.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/update.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/validate.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/welcome.png
ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/sequin.htm
ncbi-tools-x11: /usr/share/lintian/overrides/ncbi-tools-x11
ncbi-tools-x11: /usr/share/menu/ncbi-tools-x11
Now, I can find the bin folder with your commands, probably I am missing
something very stupid here, but I can't seem to locate the /lib for the
tools, which is what I need to set in the Vicuna config file before running
make.
And before testing Tim suggestion to run the
/executable/vicuna-omp.static.linux64
I need to run the make file, after have set the /lib, if this make sense.
It seems that since the package is there, I should been able to locate the
"/lib" for it... I have also went inside each folder linked above but only
finding the executable or the bin.
Do you have any other suggestion? I am very thankful for all the advice and
time you're spending I still have lots to learn so some things that might
be obvious are not for me.
Thank you so much again
regards
Flavia
2016-02-23 17:41 GMT+00:00 Tony Travis <tony.travis at minke-informatics.co.uk>
:
> On 23/02/16 16:55, Flavia Flaviani wrote:
> > [...]
> > 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?
>
> Hi, Flavia.
>
> First, check that you have the package installed:
>
> > dpkg -l ncbi-tools-x11
> > Desired=Unknown/Install/Remove/Purge/Hold
> > |
> Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
> > |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
> > ||/ Name Version Architecture
> Description
> >
> +++-===========================-==================-==================-===========================================================
> > ii ncbi-tools-x11 6.1.20120620-7 amd64
> NCBI libraries for biology applications (X-based utilities)
>
> Then, check where the files are installed:
>
> > dpkg -L ncbi-tools-x11
> > /.
> > /usr
> > /usr/lib
> > /usr/lib/mime
> > /usr/lib/mime/packages
> > /usr/lib/mime/packages/ncbi-tools-x11
> > [...]
>
> Or, you can find all the packages that installed 'ncbi-tools-x11':
>
> > dpkg -S ncbi-tools-x11
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/authors.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/submit.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firewall.html
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/changelog.Debian.gz
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/welcome.png
> > app-install-data:
> /usr/share/app-install/desktop/ncbi-tools-x11:Cn3D-3.0.desktop
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/logo.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/annot.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/loc_page.png
> > ncbi-tools-x11: /usr/share/lintian/overrides/ncbi-tools-x11
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/sequence.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing1.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/contact.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/affil.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/copyright
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/graphic.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/desktop.png
> > app-install-data:
> /usr/share/app-install/desktop/ncbi-tools-x11:ddv.desktop
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing2.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.gz
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.sequin.gz
> > ncbi-tools-x11: /usr/lib/mime/packages/ncbi-tools-x11
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein1.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/format.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firedialog.gif
> > ncbi-tools-x11: /usr/share/menu/ncbi-tools-x11
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/ncbi_sequin.css
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucset.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucaln.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/cds_edit.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/genbank.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein2.png
> > app-install-data:
> /usr/share/app-install/desktop/ncbi-tools-x11:entrez2.desktop
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/update.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/validate.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/organism.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/props_pg.png
> > app-install-data:
> /usr/share/app-install/desktop/ncbi-tools-x11:udv.desktop
> > app-install-data:
> /usr/share/app-install/desktop/ncbi-tools-x11:Psequin.desktop
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/sequin.htm
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/net_cfg.png
>
> You can also search the entire repository using:
>
> > sudo -i
> > apt update
> > apt install apt-file
> > apt-file update
> > apt-file search ncbi-tools-x11
> > ajt at beluga:~$ apt-file search ncbi-tools-x11
> > app-install-data:
> /usr/share/app-install/desktop/ncbi-tools-x11:Cn3D-3.0.desktop
> > app-install-data:
> /usr/share/app-install/desktop/ncbi-tools-x11:Psequin.desktop
> > app-install-data:
> /usr/share/app-install/desktop/ncbi-tools-x11:ddv.desktop
> > app-install-data:
> /usr/share/app-install/desktop/ncbi-tools-x11:entrez2.desktop
> > app-install-data:
> /usr/share/app-install/desktop/ncbi-tools-x11:udv.desktop
> > med-bio: /usr/share/blends/med/menu/ncbi-tools-x11
> > ncbi-tools-x11: /usr/lib/mime/packages/ncbi-tools-x11
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.gz
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.sequin.gz
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/changelog.Debian.gz
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/copyright
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firedialog.gif
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firewall.html
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/affil.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/annot.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/authors.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/cds_edit.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/contact.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/desktop.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/format.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/genbank.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/graphic.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/loc_page.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/logo.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/ncbi_sequin.css
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/net_cfg.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucaln.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucset.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing1.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing2.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/organism.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/props_pg.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein1.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein2.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/sequence.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/submit.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/update.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/validate.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/welcome.png
> > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/sequin.htm
> > ncbi-tools-x11: /usr/share/lintian/overrides/ncbi-tools-x11
> > ncbi-tools-x11: /usr/share/menu/ncbi-tools-x11
>
> HTH,
>
> 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
> _______________________________________________
> Bio-Linux-list mailing list
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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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