Hi Marcel, On Thu, Dec 1, 2011 at 11:28 AM, Marcel Schumann < schumann@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<greg@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: schumann@informatik.uni-**tueb**ingen.de <http://tuebingen.de><; schumann@informatik.**uni-tuebingen.de<schumann@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: schumann@informatik.uni-**tuebingen.de<schumann@informatik.uni-tuebingen.de>