Problems running galaxy Cloudman at Amazon

Question: Problems running galaxy Cloudman at Amazon

12 months ago by

clizama • 0 wrote:

Hi,

I used to use galaxy in amazon web services (from UCDAVIS). Looks like the public AMI is not running property anymore.

I was wondering if has any other public AMI in amazon web services to run a galaxy instances or in other cloud.

I was trying to use cloudman to run a galaxy instances in amazon web services, but I have to open and account in portalxsede but my IP is closing the lab soon (portalxsede required a PI to give you a allocation).

Thanks If some one know where I can run galaxy should be really useful.

admin aws cloudman galaxy • 667 views

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modified 11 months ago • written 12 months ago by clizama • 0

12 months ago by

Enis Afgan • 690

United States

Enis Afgan • 690 wrote:

How are you trying to use the AMI? If you're using the AWS dashboard directly, that's not the correct method - CloudLaunch should be used instead: https://beta.launch.usegalaxy.org/catalog/appliance/galaxy-cloud

ADD COMMENT • link written 12 months ago by Enis Afgan • 690

11 months ago by

clizama • 0

clizama • 0 wrote:

Hi Enis,

I'm using the option that you send me but I'm trying to install new tools in the galaxy. Looks Like my user dosent have the tools shed. Not sure how to get tophat and all this inside of galaxy.

Thanks Carlos

ADD COMMENT • link written 11 months ago by clizama • 0

11 months ago by

Enis Afgan • 690

United States

Enis Afgan • 690 wrote:

You'll need to make yourself a Galaxy admin user to be able to install tools. Detailed docs are available here: https://galaxyproject.org/cloudman/services/galaxy/#becoming-a-galaxy-admin-user

ADD COMMENT • link written 11 months ago by Enis Afgan • 690

11 months ago by

clizama • 0

clizama • 0 wrote:

Just to be sure:

To create and admin account: - I have to connect to my galaxy cloud IP address through ssh in ubuntu. - I have to edit the galaxy.ini.sample (add my user together with the others) - Rename galaxy.ini.sample to galaxy.ini - Reboot the Instance through amazon aws

If I'm right:

I have one question:

When I generate my Key ID and AWS secret key. I didnt get a ssh key, that means I have to generate a ssh key in amazon aws link the key with instances and then download it and used in ubuntu to be able to connect or has a easy way to connect and modify the file without generate the ssh key.

ADD COMMENT • link written 11 months ago by clizama • 0

No need to ssh, the screenshot in the linked page (https://galaxyproject.org/cloudman/services/galaxy/#becoming-a-galaxy-admin-user) is showing the CloudMan Admin page where you just need to enter the email address with which you have registered on you Galaxy instance and click the 'Set admin users' button.

ADD REPLY • link written 11 months ago by Enis Afgan • 690

Thank you, Now is working.

I have one question:

What determine the number of task that galaxy run at the same time:

For example: when I was running the FASTQC, Galaxy run just one at the time but when I was running the trimmer software it run 7 at the same time. Now with the alignment tool is doing one at the time again.

Thanks

ADD REPLY • link written 11 months ago by clizama • 0

Some jobs are configured to use multiple CPUs at the same time, this is the list of tools (also linked from the Galaxy home page on your instance): https://github.com/galaxyproject/ansible-cloudman-galaxy-setup/blob/master/files/galaxy/job_conf.xml.cloud#L31

ADD REPLY • link written 11 months ago by Enis Afgan • 690

Has any way to change the order:

I'm running tophat, its doing one job at the time not sure if I can set-up galaxy to run more than one job at the time (with top-hat) or other tools.

ADD REPLY • link modified 11 months ago • written 11 months ago by clizama • 0

I realized if I start more working nodes the other tophat job start running.

Question: If I run more working nodes, that means I started new instances in Amazon AWS and I get charge double or triple, depends how many node I start?

Thanks Carlos

ADD REPLY • link written 11 months ago by clizama • 0

Exactly. Each new instance you start costs however much that instance type is valued by Amazon (https://aws.amazon.com/ec2/pricing/on-demand/).

ADD REPLY • link written 11 months ago by Enis Afgan • 690

Finally I open other node. I'm still I don't understand when I check in the cloudman. The new nodes has 60% por load, but the master node is just 4% load, that means all the jobs is doing by the new Node and the master basicaly is not doing nothing?

ADD REPLY • link written 11 months ago by clizama • 0

By default, as soon as you add a worker, running jobs on the master is disabled because it needs to act as the support backbone for the workers, which imposes stress on the system (e.g., the network file system service). You can enable running of jobs on the master manually from the CloudMan admin page by clicking the Switch master to run jobs link toward the bottom of the page.

ADD REPLY • link written 11 months ago by Enis Afgan • 690

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