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Old 10-01-2014, 11:29 AM   #1
Kimist99
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Default Problems with Bio-linux/Ubuntu 14.04

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!
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Old 10-01-2014, 02:17 PM   #2
Bukowski
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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

Last edited by Bukowski; 10-01-2014 at 02:21 PM.
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Old 10-01-2014, 02:27 PM   #3
Kimist99
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Quote:
Originally Posted by Bukowski View Post
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!
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Old 10-02-2014, 06:23 AM   #4
Kimist99
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Default 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
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Old 10-03-2014, 01:14 AM   #5
dpryan
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Why not just install packages as you need them directly in Ubuntu? That'd save the hassle.
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Old 10-03-2014, 05:36 AM   #6
Kimist99
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Quote:
Originally Posted by dpryan View Post
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
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Old 10-03-2014, 05:50 AM   #7
amitm
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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.
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Old 10-03-2014, 06:13 AM   #8
Kimist99
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Quote:
Originally Posted by amitm View Post
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!
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Old 10-03-2014, 06:30 AM   #9
GenoMax
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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/
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Old 10-03-2014, 06:57 AM   #10
Kimist99
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Quote:
Originally Posted by GenoMax View Post
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.
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Old 10-03-2014, 07:14 AM   #11
amitm
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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/

Last edited by amitm; 10-03-2014 at 07:17 AM. Reason: clarification
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Old 10-03-2014, 07:23 AM   #12
GenoMax
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Since the error seems to be about a missing file:

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

Code:
$ sudo touch /usr/bin/update-menus
followed by the purge.

Ref this thread: http://serverfault.com/questions/179...l-script-fails
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Old 10-03-2014, 07:54 AM   #13
Kimist99
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Quote:
Originally Posted by GenoMax View Post
Since the error seems to be about a missing file:



try

Code:
$ 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.
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Old 10-03-2014, 09:51 AM   #14
GenoMax
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Try the solution described here: http://www.bcat.eu/blog/remove-broke...ubuntu-debian/
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Old 10-03-2014, 06:00 PM   #15
Kimist99
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Quote:
Originally Posted by GenoMax View Post
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
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Old 04-24-2015, 03:39 AM   #16
cement_head
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Quote:
Originally Posted by Kimist99 View Post
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
To install Bio-Linux on top of an existing Ubuntu installation (14.04) you need to follow the instructions here: http://environmentalomics.org/bio-linux-installation/

You CANNOT simply install packages you want, it won't work, as they are are associated with each other (in Bio-Linux).
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Old 04-24-2015, 04:25 AM   #17
Kimist99
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Quote:
Originally Posted by cement_head View Post
You CANNOT simply install packages you want, it won't work, as they are are associated with each other (in Bio-Linux).
I posted an error I encoutnered installing Bio-Linux and another member kindly showed me a solution. I then posted the exact code I used to run the software which is working perfectly for me.

Perhaps you should reread the entire thread since your assumption about everything that was done starting at the post #2, appears incorrect.

Last edited by Kimist99; 04-24-2015 at 04:29 AM.
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