authentication problem with NX client for windows

[Michael Matiasek]

Hi,

I have connected to the CloudBioLinux Ubuntu 11.10 64bit 20111212 (ami-
fb00ca92) imstance with winscp without any problems. I initially tried
to run some Phylip commands from the command terminal but realized
they were likely not working since the commands required additional
user input and my command terminal explicitly states not to run any
commands that require user imput. Then I figured I needed to use the
NX client for windows. I installed the software and managed to get
through a couple different errors and now the error I am stuck on is
that I cannot authenticate. When I log in with winscp I use the
username "ubuntu" and I create a password. When i use that password in
NX client, it states: " authentication failed for user ubuntu". Any
help with this would be greatly appreciated.

Thanks

Mike

[Brad Chapman]

Mike;
The NX client requires some configuration on the CloudBioLinux instance
to open up authentication. There are 3 different ways you can do this:

- If you already have an instance running, run the script
'configure_freenx.sh' in the ubuntu user directory.

- When starting CloudBioLinux from the EC2 console, pass in user-data
with the password you want for NX access:

freenxpass: your_password

- Use BioCloudCentral (http://biocloudcentral.org), which will
start and configure the instance for password access with NX.

Hope one of these work for you. Let us know if you run into any
problems,
Brad

[Michael Matiasek]

Great thanks for your response. I am under the impression that this
is still quite new so here is some feedback so that other noobs like
me can hopefully get in and get comfortable quicker:

Just an PYI, the script mentioned above does not work, and error
message came up saying that it did not exist. However I can see the
file in the ubuntu directory. Also I am not clear on how to "pass in"
user data in the EC2 console.

I managed to get it to work via the biocloudcentral page. Though it
was not obvious that ubuntu was still the user name.

[Brad Chapman]

Mike;
Glad that BioCloudCentral got things working and thanks for the
feedback. We are currently working on some additional detailed
step-by-step documentation which will hopefully improve the experience.

> Just an PYI, the script mentioned above does not work, and error
> message came up saying that it did not exist. However I can see the
> file in the ubuntu directory.

To run scripts from a local directory you either explicitly specify the
file in the directory (since the current directory is not on your PATH):

./configure_freenx.sh

or run it directly with the shell:

sh configure_freenx.sh

> Also I am not clear on how to "pass in"
> user data in the EC2 console.

The CloudMan documentation has some details on this in the User Data section:

http://wiki.g2.bx.psu.edu/Admin/Cloud#Customizing_your_cloud_cluster

The user data box is one of the options in the EC2 console wizard as you
start an instance.

> I managed to get it to work via the biocloudcentral page. Though it
> was not obvious that ubuntu was still the user name.

Sorry for the confusion. I updated the monitor page on BioCloudCentral
to be more explicit about the NX client settings.

Thanks again,
Brad

[Brad Chapman]

Mike;

> Thanks again for your help. I am having trouble getting ARB to work in
> the most recentAMI (CloudBioLinux Ubuntu 11.10 64bit 20111212
> (ami-fb00ca92)). I found the documentation page here
> <http://nebc.nerc.ac.uk/tools/bioinformatics-docs/faq#arb>and here
> <http://nebc.nerc.ac.uk/tools/bio-linux/userguide#groups>to get arb
> working properly but I am having trouble getting this to work. When I
> open the users and groups and then click on manage groups, I do not find
> "arb" in the list of groups. Could you help me to get ARB operational
> on my instance?

Unfortunately I don't have any experience with ARB so am cc'ing the
CloudBioLinux list. Hopefully someone there can be of more help.

Right now ARB is not included on the CloudBioLinux images, since it
depends on the libmotif3 library:

bio-linux-arb : Depends: libmotif3 but it is not installable

This has moved to libmotif4 on 11.10 so the package will need an
update. It sounds like this one is a bit tricky so hopefully on of the
Bio-Linux folks with more experience with the package can chime in.

Thanks,
Brad

[Michael Matiasek]

Thanks for your response Brad. I did not realize there was a difference
between cloudbiolinux and bio-linux... hopefully ARB will be coming to
the cloud soon.

Mike

[Tim Booth]

Hi All,

ARB is still being supported for Debian as a legacy application, but has
not made it to Ubuntu. ARB is regarded as legacy because it requires
the Motif libraries which went out of fashion some time in the 90s.

As a quick fix it may be possible to load the .deb files from Debian Sid
directly onto CloudBioLinux - you'd need to get the four debs (arb,
arb-common, arb-doc, libarb) from this page:
http://packages.debian.org/source/sid/arb

Then download them to a directory on your CBL instance and do 'sudo dpkg
-i *.deb'. If that fails then I'll try to do a custom compilation some
time this week.

Cheers,

TIM

--
Tim Booth <tbo...@ceh.ac.uk>
NERC Environmental Bioinformatics Centre

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB

http://nebc.nerc.ac.uk
+44 1491 69 2705

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