I think you are experiencing this bug, which is a major problem with the latest
AMI.
https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to-mnt
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of
I tried this method again and it still does not work. The only items in /mnt
are the directories cm and lost+found.
From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Thursday, August 01, 2013 4:48 PM
To: Ravpreet Setia
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re
Anatoly, did this method work for you? It is not working for me.
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Dannon Baker [dannon.ba...@gmail.com]
Sent: Wednesday, August 07, 2013 8:00 PM
To: Ulyanov_Anatoly
Cc:
as the tool volume update..
Thanks
From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Thursday, August 08, 2013 4:40 PM
To: Ravpreet Setia
Cc: Ulyanov_Anatoly; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy on cloud config issues
Ravpreet -- can you
continue the discussion on the other thread. Thanks!
From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Thursday, August 08, 2013 5:08 PM
To: Ravpreet Setia
Cc: Ulyanov_Anatoly; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy on cloud config issues
On Thu, Aug
In the form, under Instances in your account I choose New Cluster. Let me
know if there are additional details you need.
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Ravpreet Setia [ravpreet.se...@oicr.on.ca]
Sent
:
['al...@ip-10-179-15-41.ec2.inte BIP 0/0/2 0.91 lx24-amd64']
[DEBUG] master:1650 2013-08-01 20:09:27,666: SS: SGE..OK;
From: Ravpreet Setia
Sent: Thursday, August 01, 2013 4:01 PM
To: Dannon Baker
Subject: RE: [galaxy-dev] Cloudman - When
]
on behalf of Ravpreet Setia [ravpreet.se...@oicr.on.ca]
Sent: Thursday, August 01, 2013 4:11 PM
To: Dannon Baker
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman - When will the symlinks be resolved ?
Here it is:
'pd.yaml' not found at paths.py load!
Set paths.P_GALAXY_HOME
I am referring to the following bug:
https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to-mnt
We are waiting for this bug to resolve before we fix any other issues with our
Cloudman scripts. I am wondering when you think this bug will be resolved so I
can plan my time.
]
on behalf of Ravpreet Setia [ravpreet.se...@oicr.on.ca]
Sent: Tuesday, July 23, 2013 7:00 PM
To: Dannon Baker
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman - is it possible to still use depreciated
AMIs ?
Hey, thanks for the response.
The ssh issue was on my end and is now
4:56 PM
To: Ravpreet Setia
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman master cannot connect to volume at start-up
Can you verify that the volume does still exist in your account, and that
you're launching from the same availability zone that the volume exists in?
On Mon
: Dannon Baker [dannon.ba...@gmail.com]
Sent: Monday, July 22, 2013 5:01 PM
To: Ravpreet Setia
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cloudman - is it possible to still use depreciated
AMIs ?
Yes, you can still use the deprecated AMIs. What error are you seeing when you
try
Nevermind, this issue was resolved once I fixed my issue with ssh'ing into
outside hosts.
Thanks.
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Ravpreet Setia [ravpreet.se...@oicr.on.ca]
Sent: Tuesday, July 23, 2013
* This is what has been reported by the cluster status log:
*
* 20:01:14 - Master starting
* 20:01:16 - Trouble getting volume reference for volume vol-91cfd1cb:
EC2ResponseError: 400 Bad RequestInvalidVolume.NotFoundThe volume
'vol-91cfd1cb' does not
I tried launching an instance specifying ami-da58aab3 as the AMI but I am
unable to SSH or access Cloudman using the instance's URL.
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Please keep all replies on the list by using reply all
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This may be a problem with the latest Galaxy Cloudman AMI.
Some tools (tophat is one) are failing to run because they cannot be found. I
have noticed that after launching a new instance with the latest AMI, the
package/version/default sym-links under /mnt/galaxy/tools point to a
directory in
to the point, is your tophat job failing due to bowtie not being found?
Try adding the path to bowtie executables to tophat's env.sh file as well and
see if that fixes the issue.
On Fri, Jul 12, 2013 at 5:26 PM, Ravpreet Setia
ravpreet.se...@oicr.on.camailto:ravpreet.se...@oicr.on.ca wrote:
This may
help would be appreciated.
Cheers,
Mo Heydarian
On Mon, Jul 8, 2013 at 5:02 PM, Ravpreet Setia
ravpreet.se...@oicr.on.camailto:ravpreet.se...@oicr.on.ca wrote:
Some tools (tophat is one) are failing to run because they cannot be found. I
have noticed that after launching a new instance
It is quite tedious to do so if you have many instances running. Is there a way
to automate this step? Thanks.
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Please keep all replies on the list by using reply all
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and other
Initially only one volume is shown on Amazon's EC2 management console. Then,
after the user goes into the instance's URL and logs into Cloudman, they are
prompted with a box called Initial cluster configuration where they specify
the size of the volume they want. THEN, three nameless volumes
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