Hi,
I am trying to change the ftp dir (and some other modifications) vs. the
standard Galaxy Cloudman config.
When I modify the appropriate line in
/mnt/galaxy/galaxy-app/universe_wsgi.ini on my running cloud instance: my
changes disappear when I terminate/restart the cluster.
When I modify
persist across CM cluster termination/restart?
It would be great to get some experienced insight on how best to
complete this configuration, and have it persist.
Any guidance would be greatly appreciated. Thanks,
David Kovalic
Hi,
I want to be able to use different AWS worker instance types than are
currently provided in the cloudman "Add worker nodes" menu.
Say for example I am interested in using AWS 'r3.*' instance types as my
workers, how can I add these to be available in the cloudman interface?
Thanks,
David
ot;Custom Instance Type" and put whatever
> you like.
>
> Best,
> Alexander
>
> 2015-09-12 11:35 GMT-05:00 David Kovalic <kova...@analome.com>:
>
>> Hi,
>>
>> I want to be able to use different AWS worker instance types than are
>> current
All,
>From my read of the command line docs for ANNOVAR I believe that the
program needs so ancillary files for its operation (e.g. GenePred file,
transcripts fasta file, etc...).
Does anyone have any experience deploying custom genomes in Galaxy for use
with ANNOVAR? Specifically what files
cengineer.blogspot.co.uk/2015/03/installing-annovar-in-galaxy.html
>
> As I recall all the databases we installed were standard ones from
> ANNOVAR. However the above instructions might be useful in at least
> getting started.
>
> Apologies if I've misunderstood your question and this doesn't
variable (set via the Galaxy job configuration), or
> if not set, defaults to using 8 threads.
>
> I've essentially rephrased the README file here - did you see
> that, or does it need more information added?
>
> Thanks,
>
> Peter
>
>
> On Tue, May 3, 2016 at 6:
Hello,
We would like to split fasta query files and run multiple concurrent jobs
to minimize our processing wall clock time for large jobs.
After chatting with folks at GCC 2015 I understand this is possible, my
problem is I cant find instructions on hos to configure
CloudMan/ncbi_blast_plus to
on these machines.
Any advice? Thanks.
David
PS. what is the path of the file which contains the split_size="1000"
configuration?
On Tue, May 3, 2016 at 2:19 PM David Kovalic <kova...@analome.com> wrote:
> Peter,
>
> Thanks, I didn't see that, I was reading the paper and searchi
galaxy/tmp/job_working_directory all of the sub-job directories
are prepared. Maybe an issue with the job scheduler/dispatch.
Thanks again.
David
On Tue, May 3, 2016 at 5:11 PM Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Tue, May 3, 2016 at 9:23 PM, David Kovalic <kova...@analome.com> wro
:
https://galaxyproject.org/cloud/jetstream/storage/That's the most
straightforward way at the moment. Changing all the configs to use the volume
would me more involved, particularly because of the database and how it gets
installed...
On Thu, Mar 9, 2017 at 4:13 PM, David Kovalic <kova...@analome.
Hi,
When we launch a Galaxy instance on Jetstream, the galaxy user's home dir is
set up on the root volume, this has inherent limitations. Is there a good way to
change the home dir location to an attached disk?
Thanks,
David___
Please keep
Peter,
Thanks.
Dan,
What is your opinion (what work needs to be done to make this
production-worthy)? Maybe if my chops are up to it I can take a crack…
David
David Kovalic Ph.D.President,Analomephone:+314.496.8808web:www.analome.comemail:
kova...@analome.com
On Fri, Aug 11, 2017 4:58 AM
Hi,
Does anyone know if a data manager exists in the tool shed for creating and
integrating NCBI BLAST+ indices within galaxy?
I can't seem to find it in the tools shed or searching the internet Surly such a
tool must exist.
Any info would be greatly appreciated.
Thanks,
David
David Kovalic
Hi,
Is it possible, and if so how, to run the galaxy devteam (version546ada4a9f43)
of bwa_mem with the "-t" option and a value >1?
"-t INT number of threads [1]"
This would be quite useful, and used, for accelerating single bwa mem jobs.
Thanks,
/blob/dev/config/job_conf.xml.sample_advanced#L791
I couldn't find more information, hope this gets you started!
Cheers,
Bjoern
Am 01.06.2017 um 20:48 schrieb David Kovalic:
> Bjoern,
>
> Thanks for the response.
>
> I agree with the first approach (admin control
this.
However, if you really want to offer this to a user, Galaxy also offers
to enable this option per tool level and will add additional parameter
fields to set GALAXY_SLOTS as a user.
Cheers,
Bjoern
Am 26.05.2017 um 20:23 schrieb David Kovalic:
> Hi,
>
> Is it
Enis,
To clarify, our credentials are in the beta system which dosn't work.
To me it seems like an aws authentication issue.
David
On Wed, Nov 8, 2017, 7:22 PM David Kovalic <kova...@analome.com> wrote:
> Enis,
>
> Yes our credentials are in the beta system.
>
> Lmk
CC'ing him in case he has additional input.
>
> On Tue, Nov 7, 2017 at 12:53 PM, David Kovalic <kova...@analome.com>
> wrote:
>
>> Enis,
>>
>> I am having issues launching previously existing clusters today, here is
>> some more info:
>>
>>-
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