Following the instructions at
http://wiki.g2.bx.psu.edu/CloudMan?action=show&redirect=Admin%2FCloud
Setup an instance using the latest AMI and did configure it to use a password
AMI: galaxy-cloudman-2012-05-10 (ami-78a00411)
Waited 10+ minutes after instance is running and going to
http://ec2
Getting up to speed on Galaxy and couldn't find examples or discussion related
to the architecture and was hoping an expert could give some quick
pointers/guidance.
Where do I find info if the installed applications make use of multiple nodes
via MPI(etc) which would indicate the benefit of sta
Started up a cluster on Amazon using the Launch a Galaxy Cloud Instance and got
the following message. Since I don't have any control over where the instances
are run not sure how I can control this. The last 4 or 5 times I have started
up an existing instance has worked with no problem.
Messag
ucket?
Any suggestions?
From: Scooter Willis mailto:hwil...@scripps.edu>>
Date: Wednesday, October 31, 2012 10:32 AM
To: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>"
mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: Amazon
Started up a cluster on Amazo
Using large amazon instance
Trying to do an interval join of SNPs as output from pileup 120,000
regions(5.5Mb) with with snp135Common 12,000,000(425Mb) and get the following
errors. The goal is to pickup rs id's for known SNPs in the list of SNPs.
Is this a memory issue?
I was able to do the o
Did a subtract first to get a known list of rs SNPs that will be found in the
tumor SNPs. That ran without error. Doing a join of the subtracted list of rs
SNPs and the tumor SNPs.
So something different in the join code then in the subtract code.
From: Scooter Willis mailto:hwil
Last night I used the Amazon console to stop my working instance. Today started
up the instance using amazon console. Waited appropriate time, using new
assigned public ip address and no response. Also did a reboot and no response.
I can ssh to the instance but do not know what to check for err
mply restart the instance via
>the AWS console and everything *should* come up fine.
>
>Sorry for any inconvenience!
>
>-Dannon
>
>
>
>On Nov 1, 2012, at 10:49 AM, Scooter Willis wrote:
>
>>
>> Last night I used the Amazon console to stop my working in
I have a new workflow setup and filter by quality on an input fastqsanger file.
I get the following error message where the original elements worked correctly.
The IP address is a compute node. I have one compute node running with
autoscaling on. Any reason why the mnt is working?
/opt/sge/def
Running a CloudMan created instance on Amazon.
Updated using cloudman from http://bitbucket.org/galaxy/galaxy-central to
version 8167:b0c916349070
Tried to run bowtie and get the following error. Searched the message archives
an someone else reported the same problem but thought it was related
ces to BlastXML. Save the file, restart galaxy, and you should be
>good to go.
>
>-Dannon
>
>On Nov 8, 2012, at 10:40 AM, Scooter Willis wrote:
>
>> Running a CloudMan created instance on Amazon.
>>
>> Updated using cloudman from http://bitbucket.org/galaxy/gal
mnt/galaxyTools/galaxy-central/datatypes_conf.xml removing any
>references to BlastXML. Save the file, restart galaxy, and you should be
>good to go.
>
>-Dannon
>
>On Nov 8, 2012, at 10:40 AM, Scooter Willis wrote:
>
>> Running a CloudMan created instance on Amazon.
&
(see the cloud admin panel).
>
>
>On Nov 8, 2012, at 11:20 AM, Scooter Willis wrote:
>
>> Ok that fixed Bowtie.
>>
>> Any thoughts on expected state of installing Abyss from toolshed. It
>> indicates no requirements so my expectation is that installing from
dmin/Config/Tool%20Dependencies) and
>then, after it has been installed, modify the abyss wrapper to include a
>abyss tag, and finally persist
>changes to galaxyTools (which will also restart Galaxy, reloading the
>tools).
>
>-Dannon
>
>
>On Nov 8, 2012, at 12:09 PM, Scooter
ould be to check and see if those files
>actually exist (and they should).
>
>If those messages are occurring on stdout and not stderr though, they
>shouldn't be causing failed jobs and something else might be wrong.
>
>-Dannon
>
>
>On Nov 8, 2012, at 1:27 PM, Scooter W
lve to
/mnt/galaxyTools/galaxy-central/tool-data/shared/ucsc/ (or ensembl, ncbi, etc)
Can you tell me the output of 'hg tip' 'hg st' and 'hg diff' from the root
/mnt/galaxyTools/galaxy-central/ ?
-Dannon
On Nov 8, 2012, at 1:41 PM, Scooter Willis
mailto:hwil...@sc
I found out about Galaxy based on the ENCODE project making a big deal about
packaging the software they used on a CD and available for download. I
misplaced the CD and following some link on an ENCODE/Nature web site found
Galaxy. What I haven't found is any public workflows that would indicate
>
>--
>James Taylor, Assistant Professor, Biology/CS, Emory University
>
>
>On Sun, Nov 18, 2012 at 10:29 AM, Scooter Willis
>wrote:
>> I found out about Galaxy based on the ENCODE project making a big deal
>>about
>> packaging the software they used on a CD and
Did you delete the S3/shapshots buckets? That is where everything is
stored and I think EBS volumes related to everything dynamic are created.
On 12/10/12 6:17 PM, "Fabiano Lucchese" wrote:
> Guys,
>
> I appreciate your effort to help me, but it looks like my AWS account
>has some se
Is the cloud man Amazon EC2 instance updated with the latest?
From: Jennifer Jackson mailto:j...@bx.psu.edu>>
Date: Thursday, December 20, 2012 8:49 PM
To: Galaxy Announce
mailto:galaxy-annou...@bx.psu.edu>>, Galaxy User
mailto:galaxy-u...@bx.psu.edu>>, Galaxy Dev
mailto:galaxy-...@bx.psu.edu>>
the cloud uses and will not
>be updating for this distribution release. Updates to the cloud
>deployment will most likely resume with the next distribution.
>
>Until then, you can always update your individual cloud instances to any
>revision you'd like.
>
>
>On
l update all galaxy tool
>wrappers (the .xml) that come with the distribution, but that's not the
>binary version (which I think you're asking about, correct me if I'm
>wrong).
>
>And, the next release will probably be in early-mid January.
>
>
>On Dec 22, 2
Used cloud man to create a new cluster on Feb 22 and picked 500GB as the
initial size of the data drive. Working with TCGA exome DNA seq data didn't
take long to fill that up. Used the cloud man admin interface to resize from
500GB to 1TB and the resize operation took 15 hours. Not sure if that
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