Problems with Bio-linux/Ubuntu 14.04

[Kimist99]

Hello everyone!

I get the following when I attempt to launch Bio-linux using a VM in Ubuntu. I'm a relative newbie to bioinformatics, so please answer accordingly. Thanks!

[Bukowski]

Why are you running Bio-Linux as a VM inside an existing Linux machine?

That might be a little redundant...

http://nebc.nerc.ac.uk/tools/bio-linux-5/other-bl-docs/package-repository#Location

[Kimist99]

Why are you running Bio-Linux as a VM inside an existing Linux machine?

That might be a little redundant...

http://nebc.nerc.ac.uk/tools/bio-lin...itory#Location

Yes.

I originally tried to download Bio without using VM but didn't have any success. But I didn't use instructions in the link you provided, so I'll give that a try and report back.

Thanks!

[Kimist99]

Still having problems

So after going throuhg the instructions above( up to step 16), I'm now getting the following error massage at the terminal:

Failed to SetCandidateRelease for unstable

I've also attached a screenshot of part of the error message window that appears next to the synaptic manager box.

Thanks again!

Kimberly

[dpryan]

Why not just install packages as you need them directly in Ubuntu? That'd save the hassle.

[Kimist99]

Why not just install packages as you need them directly in Ubuntu? That'd save the hassle.

DId that for a number of packages including the following (bio-linux-arb), then received the message that bio-linux-fasta would need to be removed (apparently I added this one first).

Package didn't install and I got the message package operation failed with the following details:

installArchives() failed:
Extracting templates from packages: 18%
Extracting templates from packages: 36%
Extracting templates from packages: 54%
Extracting templates from packages: 72%
Extracting templates from packages: 90%
Extracting templates from packages: 100%
Preconfiguring packages ...

Extracting templates from packages: 18%
Extracting templates from packages: 36%
Extracting templates from packages: 54%
Extracting templates from packages: 72%
Extracting templates from packages: 90%
Extracting templates from packages: 100%
Preconfiguring packages ...

Extracting templates from packages: 18%
Extracting templates from packages: 36%
Extracting templates from packages: 54%
Extracting templates from packages: 72%
Extracting templates from packages: 90%
Extracting templates from packages: 100%
Preconfiguring packages ...
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 363774 files and directories currently installed.)
Removing bio-linux-cdbfasta (1:20100722bl-3) ...
Finished removing Bio-Linux package: bio-linux-cdbfasta
/var/lib/dpkg/info/bio-linux-cdbfasta.postrm: 3: /var/lib/dpkg/info/bio-linux-cdbfasta.postrm: /usr/bin/update-menus: not found
dpkg: error processing package bio-linux-cdbfasta (--remove):
subprocess installed post-removal script returned error exit status 127
Error in function:

I then used the following sudo apt-get purge bio-linux-cdbfasta, to try to remove the bio-linux-cdbfasta then received the message:

Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
bio-linux-cdbfasta
0 upgraded, 0 newly installed, 1 to remove and 21 not upgraded.
1 not fully installed or removed.
After this operation, 311 kB disk space will be freed.
Do you want to continue? [Y/n] y
(Reading database ... 363774 files and directories currently installed.)
Removing bio-linux-cdbfasta (1:20100722bl-3) ...
Finished removing Bio-Linux package: bio-linux-cdbfasta
/var/lib/dpkg/info/bio-linux-cdbfasta.postrm: 3: /var/lib/dpkg/info/bio-linux-cdbfasta.postrm: /usr/bin/update-menus: not found
dpkg: error processing package bio-linux-cdbfasta (--remove):
subprocess installed post-removal script returned error exit status 127
Errors were encountered while processing:
bio-linux-cdbfasta
E: Sub-process /usr/bin/dpkg returned an error code (1)

Now I'm stuck after hours of troubleshooting,

Thanks in advance for your help

[amitm]

hi Kimist99,
What analysis are you trying to do after you have installed BioLinux? Maybe you could ask about the relevant analysis software which would be more pertinent for this forum.
OS installation issues would get better addressed elsewhere.

[Kimist99]

hi Kimist99,
What analysis are you trying to do after you have installed BioLinux? Maybe you could ask about the relevant analysis software which would be more pertinent for this forum.
OS installation issues would get better addressed elsewhere.

Thank you for your response.

I'm very familiar with most of the major bioinformaics software out there, I simply wanted to expand my knowledge base as I'm also a 1st year PhD student in Bioinformatics. I'm also relatively new to SEQanswers.

If there's a better place for this question other than in the bioinformatics forum by all means, do tell me where that is.

Thanks again!

[GenoMax]

Wonder if part of the problems are because of 32-bit packages. I am reasonably certain that you are running a 64-bit OS. Corresponding 64-bit bio-linux packages are at this link: http://nebc.nerc.ac.uk/bio-linux/dis.../binary-amd64/

[Kimist99]

Wonder if part of the problems are because of 32-bit packages. I am reasonably certain that you are running a 64-bit OS. Corresponding 64-bit bio-linux packages are at this link: http://nebc.nerc.ac.uk/bio-linux/dis.../binary-amd64/

Thanks for the info.

Unfortunately, I'm still getting the same error as earlier regarding the removal of bio-linux-cdbfasta.

[amitm]

hi,
That error might be due to a circular dependency problem. If you did all installation steps till now (for BioLinux) through cmdline (using apt), then try uninstalling pkgs installed earlier than cdb-fasta and then try or put evrything in one line and uninstall all [The pkgs installd would be available in order in the bash history]. Should work definitely.
Sorry I couldnt give a better solution.

You might want to try the VM file for BioLinux available from download here.

http://environmentalomics.org/bio-linux-installation/

[GenoMax]

Since the error seems to be about a missing file:

/var/lib/dpkg/info/bio-linux-cdbfasta.postrm: 3: /var/lib/dpkg/info/bio-linux-cdbfasta.postrm: /usr/bin/update-menus: not found

try

$ sudo touch /usr/bin/update-menus

followed by the purge.

Ref this thread: http://serverfault.com/questions/179...l-script-fails

[Kimist99]

Since the error seems to be about a missing file:



try

$ sudo touch /usr/bin/update-menus

followed by the purge.

Ref this thread: http://serverfault.com/questions/179...l-script-fails

I definitely have a half-install issue with bio-linux-cdbfasta. I tried the solution you posted and I'm getting the same error message as before.

[GenoMax]

Try the solution described here: http://www.bcat.eu/blog/remove-broke...ubuntu-debian/

[Kimist99]

Try the solution described here: http://www.bcat.eu/blog/remove-broke...ubuntu-debian/

Worked like a charm, thanks a bunch.

Here's the code I used:

sudo mv /var/lib/dpkg/info/bio-linux-cdbfasta.* /tmp/
sudo dpkg --remove --force-remove-reinstreq bio-linux-cdbfasta