Hi Marcel,

On Thu, Dec 1, 2011 at 11:28 AM, Marcel Schumann <
schum...@informatik.uni-tuebingen.de> wrote:

> Hi Enis,
>
> well, I know I do not have to create a new AMI if I want to reuse an
> instance myself.
>
> However, I would like to share the modified GalaxyCloudman version with
> other people and therefore I do have to create an AMI.
>
Unless you modify the system packages (i.e., your customizations are not
self contained), you still don't have to create a new AMI to share a
cluster. There is the share-a-cluster option (icon next to the cluster
name). Just wanted to make sure you were aware of the functionality...


> Ok, I will try to make this work somehow ... but I guess there are no
> immediate clues as to what could have gone wrong? Or do you have any ideas
> what I should try?
>
CloudMan sets up the system at runtime so it performs changes that then get
persisted when you create the AMI. So, it is necessary to reverse those
changes before creating the AMI so that next time a cluster is started, the
startup procedure proceeds as before. Did you see what's in the cloudman
log (/mnt/cm/paster.log) on your customized AMI? That's probably the
easiest place to start and we can work from there.

Enis



>
> Cheers,
> Marcel
>
>
>
> On 12/1/11 10:45 AM, Enis Afgan wrote:
>
>> Hi Marcel,
>>
>> However, when I create an AMI, terminate the cluster and create a new
>>
>>> cluster using the new AMI, both /mnt/galaxyData and /mnt/galaxyTools do
>>> not
>>> exist anymore, i.e. /dev/sdg3 and /dev/sdg4 are not mounted
>>> automatically.
>>> If I mount those two devices manually, everything runs smoothly again.
>>>
>>> So, is there anything that I might have forgotten to do while creating
>>> the
>>> AMI? Is there a way to make sure that those devices will be mounted
>>> automatically?
>>>
>>> It is not necessary to create a new AMI when wanting to customize your
>>>
>> cluster. Instead, on the admin interface - after you have modified the
>> file
>> systems, there is an option to persist static file systems (galaxyTools&
>> galaxyIndices). Once the process is completed and you restart the cluster,
>> just continue to use the same AMI. CloudMan will use the new, customized,
>> data snapshots at runtime.
>>
>> Let us know how it goes,
>> Enis
>>
>>
>>  Regards,
>>> Marcel
>>>
>>>
>>>
>>> On 11/30/11 3:57 PM, Enis Afgan wrote:
>>>
>>>  Hi Marcel,
>>>> It would be best to use 'galaxy' user to add any tools. To do so, after
>>>> you've logged in as ubuntu user, simply execute:
>>>> sudo su galaxy
>>>> and you will become galaxy user. You can then make the desired
>>>> modifications.
>>>>
>>>> Good luck,
>>>> Enis
>>>>
>>>> On Wed, Nov 30, 2011 at 3:42 PM, Greg Von Kuster<g...@bx.psu.edu>
>>>> wrote:
>>>>
>>>>  Hello Marcel,
>>>>
>>>>
>>> --
>>> Marcel Schumann
>>>
>>> University of Tuebingen
>>> Wilhelm Schickard Institute for Computer Science
>>> Division for Applied Bioinformatics
>>> Room C313, Sand 14, D-72076 Tuebingen
>>>
>>> phone:  +49 (0)7071-29 70437
>>> fax:  +49 (0)7071-29 5152
>>> email:  schum...@informatik.uni-**tueb**ingen.de <http://tuebingen.de><
>>> schumann@informatik.**uni-tuebingen.de<schum...@informatik.uni-tuebingen.de>
>>> >
>>>
>>>
>>
>
> --
> Marcel Schumann
>
> University of Tuebingen
> Wilhelm Schickard Institute for Computer Science
> Division for Applied Bioinformatics
> Room C313, Sand 14, D-72076 Tuebingen
>
> phone:  +49 (0)7071-29 70437
> fax:  +49 (0)7071-29 5152
> email:  
> schum...@informatik.uni-**tuebingen.de<schum...@informatik.uni-tuebingen.de>
>
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