Hi Jeremy,
a) Yes, were are using a custom build and the build shows the correct
number of contigs (28.592).
b) There are no errors in the console.
Thanks, Thomas
Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Gesendet: Dienstag, 22. Oktober 2013 15:55
An: Berner, Thomas
Cc: ga
The good news is that it sounds like the build has been set up correctly; the
bad news is that a lack of console errors gives us nothing else to go on.
Would you be interested in sharing your datasets with me and I can take a look?
Also, our next release is coming next week, and there are some b
Hi all,
I have created a Data library and uploaded (linked) some fastq files.
After applying the bar code splitter tool, when I click on the output links
I can get the output on my browser. I also get them by copy pasting the
address in a new tab. But when I try the upload via URL by copy pasting
I have created a Trello card for this (https://trello.com/c/m2x1CXmi)
and I have attached a more flushed out IRC conversation for additional
public comment/posterity. I think this is exciting stuff - though I
need to get my head around mesos and how it would interact with Galaxy
more fully. I think
Kyle
This is something I am very interested in. The three parts below make sense to
me. I would be very happy to discuss further and provide any help to move this
forward.
Regards
On Oct 26, 2013, at 2:43 PM, Kyle Ellrott wrote:
> I think one of the aspects where Galaxy is a bit soft is the ab
I am trying to upload a bam file for my data analysis (size is about 9GB)
I am trying URL method to up load and getting error message, can you please
help me to sort out this problem. I am seeing following message
"An error occurred setting the metadata for this dataset. You may be able
to set it
I am having problems getting ProFTP to work:
This is the output of ProFTP:
FTP session opened.
manager proftpd[33551] manager (155.240.187.111[155.240.187.111]):
dispatching PRE_CMD command 'USER username' to mod_core
manager proftpd[33551] manager (155.240.187.111[155.240.187.111]):
dispatching
I don't think implementation will be very difficult. The bigger question is
this a technology people are open to?
The nearest competitor is YARN (
http://hadoop.apache.org/docs/current/hadoop-yarn/hadoop-yarn-site/YARN.html).
Mesos seems a bit more geared toward general purpose usage (with several
Hi Kyle,
We have a similar ongoing development wherein we are working on integrating
our Swift framework ( swift-lang.org ) with Galaxy. The goal is to enable
Galaxy based applications to run on a variety of distributed resources via
various integration schemes as suitable to application and under
You probably are a good person to get an opinion from. My plan isn't to
write new frameworks, but rather use existing libraries that can
communicate with Mesos to setup their parallel environments.
But for Swift, you would probably want to write a new framework. Just
looking at Swift, I imagine one
> Why are Custom Builds only enabled if you're *not* using remote_user ?
> Is this because they're related to user preferences (as per the code in
> lib/galaxy/webapps/galaxy/controllers/user.py)?
This may be an artifact of a time when user preferences were immutable. Do
Custom Builds and Prefere
Hi All,
The short version of my problem is that I often seem to find myself in a
situation where my tool gets stuck in the "Installing" phase ... and I don't
know how to get feedback on it to see where it is failing. What I guess I'm
after is just the stdout of the tool installation .. but sin
Hi Ira,
I can reproduce that error here, will try to study it tomorrow more
deeply. For the meantime can you try to remove the following lines?
It's not necessary.
Will get back to you tomorrow.
Bjoern
> Hi All,
>
> The
Hi Bjoern,
Thanks ... I thought I had to do that in order to make the GALAXY_RUBY_HOME
variable available ... nice that it's not necessary.
I've updated the tool on the test toolshed and have rerun my test but
unfortunately the problem is still there.
Cheers
Ira
On 29/10/2013, at 10:06 AM,
dear all,
There have been a few posts lately about doing distributed computing via Galaxy
- i.e.
job splitters etc - below a contribution of some ideas we have developed
and applied in our work, where we have arranged for some Galaxy tools to
execute in parallel
on our cluster.
We have develope
Hi Greg,
what I mean is that I don't expect any other errors in my files since I
corrected the errors you reported. When using my XML editor I also don't get
any errors, so the files seem OK. However, the problem remains: one of the
tools and also the dependencies definitions don't appear in th
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