Hey Dannon,
I am using Galaxy (Cloudman) to analyze RNA seq data. I have a bunch of
datasets that I ran TopHat on. I am now trying to run Cufflinks etc. I used the
same data and workflow yesterday to run Cufflinks etc and that worked fine. I
used my own reference annotation (Homo sapiens hg38)
Actually, both of these help. I'm putting a boto.conf file into
/mnt/galaxy/galaxy-app and setting the BOTO_PATH environment variable from
the python script that needs it, so it will work in dev (non-clusterman
setup) and production.
Jim
On Fri, Apr 25, 2014 at 11:20 AM, Dannon Baker wrote:
> A
Ahh, sorry about that, I misread the bit about it actually needing to be in
the user's directory. You could use a worker_post_start_script to
configure things like this (creating/copying .boto at boot from the shared
space in the script). See
https://wiki.galaxyproject.org/CloudMan/UserDatafor ho
Hi Jim,
/mnt/galaxy is shared via NFS with all cluster workers -- this (or a
subdirectory) should work for you.
-Dannon
On Fri, Apr 25, 2014 at 10:56 AM, Jim McCusker
wrote:
> Hi all,
>
> I need to add a .boto file to the user that galaxy jobs get exec'ed as on
> cloudman nodes. I thought it w
Hi all,
I need to add a .boto file to the user that galaxy jobs get exec'ed as on
cloudman nodes. I thought it would copy over what the galaxy server has in
its home directory, but that doesn't seem to happen. How can I get things
like my .boto file to migrate over to new cloudman nodes when they
Do you have Cloudman admin access on this instance?
The first thing I'd check would be http:///cloud to verify
that your instance has free disk space and to look for any errors in the
log. Then, check out the admin service list
(http:///cloud/admin)
to see if there are any service issues. Next t
Hey Alessia,
I'd love to help, but I need a little more context here. Where are you
seeing this error, what exactly are you doing when it appears, and can you
tell me a little bit more about the Galaxy configuration you're working
with?
-Dannon
On Thu, Apr 24, 2014 at 8:37 PM, Jennifer Jackson
Posting to the galaxy-...@bx.psu.edu mailing list.
https://wiki.galaxyproject.org/MailingLists
My instance of Galaxy seems to be stuck (same place since last night)
and I have received the error message several times now.
Pasting the error message below:
*Details*
user
username
Tophat works for you, even after doing this it fails to
>> run properly for me. However, at least now Galaxy can find the programs.
>>
>>
>> From: Mohammad Heydarian
>> Date: Fri, 12 Jul 2013 14:21:23 -0400
>> To: Microsoft Office User
>> Cc: Enis Afgan ,
wever, at least now Galaxy can find the programs.
>
>
> From: Mohammad Heydarian
> Date: Fri, 12 Jul 2013 14:21:23 -0400
> To: Microsoft Office User
> Cc: Enis Afgan , Galaxy-dev
> Subject: Re: [galaxy-dev] Galaxy CloudMan release - Tophat does not work
>
> Cufflink
y-dev
mailto:galaxy-...@bx.psu.edu>>
Subject: Re: [galaxy-dev] Galaxy CloudMan release - Tophat does not work
Cufflinks, Cuffcompare, and Cuffdiff are also failing to run because they can
not be found. I am using the newly released version of Cloudman 2.0
(ami-118bfc78).
Any help would
e default symlink is used by Galaxy:
> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
>
> Thanks for any suggestions.
>
>
>
> From: Enis Afgan
> Date: Sun, 30 Jun 2013 07:37:46 +0200
> To: Galaxy-dev
> Subject: [galaxy-dev] Galaxy CloudMan release
>
> *Last
*Last night, we released an update to Galaxy CloudMan.* CloudMan offers an
easy way to get a personal and completely functional instance of Galaxy in
the cloud in just a few minutes, without any manual configuration.
*IMPORTANT - please read*
Any new cluster will automatically start using this ver
I wanted to update CloudMan to use nginx 1.4.0 for web socket proxy
support, but I hit a problem. nginx-upload-module does not work with
nginx 1.4.0 and the author has no intention of continuing work on the
module.
https://github.com/vkholodkov/nginx-upload-module/issues/41
There is a patch that
On Nov 12, 2012, at 10:23 AM, Jorrit Boekel wrote:
> I was therefore looking for fault tolerance mechanisms in the galaxy project,
> which I seem to remember existed. Somehow I can't find anything about it
> right now though.
>
> I've tested a little bit, and it seems that as soon as one reboo
Dear list,
I would like to start using Amazon's spot pricing model for my
Galaxy/Cloudman instances (e.g. an on demand master node with spot instance
worker nodes). However, this means that Amazon at times of spot prices
higher than my set price limit will shutdown my instances without notion.
I
Hi, all
I just tried installing galaxy in amazon cloud following the instruction
here:http://wiki.g2.bx.psu.edu/CloudMan.
Using this ami-da58aab3, I do not have http service after the instance
is started. I logined into the instance and confirmed it. How should I
troubleshoot it?
Could your g
running multiple Galaxy Cloudman instances to circumvent
the 1 TB limit.
If I find some time I will redo the exercise with the LVM.
Kind Regards
Yves
From: Enis Afgan [mailto:eaf...@emory.edu]
Sent: Sunday, 19 February 2012 23:50
To: Wetzels, Yves [JRDBE Extern]
Cc: galaxy-dev@lists.
Hi Yves,
When you create the LVM file system - are you composing it from the volume
that already contains the data (i.e., directory structure++ created by
CloudMan) and then adding another volume into the LVM or starting with 2
new, clean volumes?
Maybe trying again and not messing with SGE at all
Hi Brad
I did not restart the master CloudMan node.
I only restarted the services (Galaxy, PostgreSQL and SGE).
I do not have these problems without creating the logical volume.
Kind Regards
Yves
Yves;
I'm hoping Enis can jump in here since he is more familiar with the
internals of CloudMan an
Yves;
I'm hoping Enis can jump in here since he is more familiar with the
internals of CloudMan and may be able to offer better advice. I can tell
you what I see from your error messages.
> I used LVM2 to create the logical volume.
Does this involve stopping and restarting the master CloudMan no
Yves;
> I am currently investigating if Galaxy Cloudman can help us in analyzing
> large NGS datasets.
>
> I was first impressed by the simple setup, the autoscaling and
> useability of Galaxy Cloudman but soon ran into the EBS limit of 1 TB L
>
> I thought to be clever and umounted the /mnt/ga
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