[ensembl-dev] Ensembl VM questions

[Matthieu Muffato]

There is a docker image with Ensembl APIs: 
https://github.com/gawbul/docker-ensembl
Note that is it not maintained by us !

Matthieu

On 27/08/15 11:31, Roy Storey wrote:
> Lurking in the background here, I’m wondering if there any plans to 
> move to a docker based distribution of these?
>
> Regards
> Roy
>
>> On 27/08/2015, at 22:01, Andrew Yates <ayates at ebi.ac.uk 
>> <mailto:ayates at ebi.ac.uk>> wrote:
>>
>> Hi G,
>>
>> We've recently been experimenting with automating our VM builds and 
>> this has brought up an interesting issue when we have multiple 
>> Ensembl virtual machine appliances imported into the same VirtualBox 
>> infrastructure. This manifested itself as us being unable to SSH onto 
>> the running machine. A quick solution is:
>>
>> sudo rm /etc/udev/rules.d/70-persistent-net.rules
>> sudo mkdir /etc/udev/rules.d/70-persistent-net.rules
>>
>> The problem is that Ubuntu remembers what MAC address it was assigned 
>> and writes this to the persistent rules file. VirtualBox, when it 
>> imports an appliance, will attempt to assign the VM the MAC address 
>> it was packaged with but will also check for MAC address collisions. 
>> When there is a collision VirtualBox assigns a new MAC address to the 
>> new appliance. Ubuntu is now confused and refuses to interface with 
>> the external network.
>>
>> Replacing the persistent rules file with a directory prevents Ubuntu 
>> from remembering as it's not possible to write a line to directory :).
>>
>> There's more information available from 
>> https://github.com/mitchellh/packer/issues/866 and you can see a 
>> shell script version of this solution with Chef's bento project at 
>> https://github.com/chef/bento/blob/master/scripts/ubuntu/networking.sh.
>>
>> We are going to put this step into our VM deployment SOP to make sure 
>> the problem doesn't arise again
>>
>> Hope this helps,
>>
>> Andy
>>
>>> On 27 Aug 2015, at 09:06, mag <mr6 at ebi.ac.uk <mailto:mr6 at ebi.ac.uk>> 
>>> wrote:
>>>
>>> Hi G,
>>>
>>> I just tested the latest VM on my Mac, downloading a fresh copy, and 
>>> had no connectivity issue.
>>> Do you get any error messages?
>>>
>>> I can resize the window, but the block inside does not change, we 
>>> will look into how to fix this for next release.
>>>
>>> As for GRCh37, you simply need to replace the default 3306 port to 
>>> 3337 to connect to the 81 release of GRCh37 databases.
>>>
>>>
>>> Regards,
>>> Magali
>>>
>>> On 26/08/2015 20:27, Genomeo Dev wrote:
>>>> Dear all,
>>>>
>>>> I am using a MAC and I have the following questions:
>>>>
>>>> - When loading the latest ensembl VM 81 into virtual box, it does 
>>>> not seem to be able to connect to the network and also the session 
>>>> can not be resized to fit the monitor. I do not have such issues 
>>>> with VM 75 for example.
>>>> - If I want to use grch37 in the latest VM (81), what is the latest 
>>>> folder ensembl-api-folder to use?
>>>>
>>>> Thanks,
>>>>
>>>> -- 
>>>> G.
>>>>
>>>>
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>
>
>
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-- 
Matthieu Muffato, Ph.D.
Ensembl Compara and TreeFam Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room  A3-145
Phone + 44 (0) 1223 49 4631
Fax   + 44 (0) 1223 49 4468

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