hi mates,
I have problems to run trinity in local galaxy, because there is no executable
script.
any ideas?
thank you very much ___
Please keep all replies on the list by using reply all
in your mail
Ok,
So I guess I need to install it locally or in the cloud to use certain tools,
right?
Thanks!
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Monday, December 16, 2013 6:55 PM
To: Javier Simon-Sanchez; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Count intervals in one file
We've run into a scenario lately where we need to run a very large workflow
(huge data in intermediate steps) many times. We can't do this because
Galaxy copies all intermediate steps to all notes, which would bog down the
servers too much.
I asked about something similar before and John
Hey Ben,
Thanks for the e-mail. I did not promise anything was coming soon, I
only said people were working on parts of it. It is not a feature yet
unfortunately - multiple people including myself are thinking about
various parts of this problem though.
I would like to respond, but I am trying
Hi John, thanks for the reply.
Yes, I mean Galaxy's default behavior of keeping all the data on all nodes
of our condor cluster. So for instance if I run a job, then the output of
that job is copied to every node in the cluster. Is this not the normal
behavior?
On Tue, Dec 17, 2013 at 9:42 AM,
Hi Nicola,
There's some bad news and good new regarding this issue.
The bad news is that the old version of the tool shed's install and test
framework required complete reengineering, and this resulted in it not being
functional in the main tool shed's environment which runs the Galaxy
Hello Jorge,
I just replied to your other question on the galaxy-user list with all
of the details about configuring tools (wrappers vs binaries).
For this tool, the binary components most likely need to be installed
and configured.
http://trinityrnaseq.sourceforge.net
Best,
Jen
Galaxy
If Galaxy just sorted these files alphabetically before display/import
would that fix your problem? Or do your users need to be able to
modify the order?
-John
On Mon, Dec 16, 2013 at 9:19 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear all
Is there a way to sort the list of files that a
John,
I can't speak for Ulf, but a more general solution would be to allow sorting by
a standard unix SORT set keys.
That would allow things like - sort by the sample ID after the 3rd dash, then
by the read direction.
-t - -k1,1n -k2,2r # http://unixhelp.ed.ac.uk/CGI/man-cgi?sort
I'm running the stable copy of galaxy and noticed that some custom,
administrative tools (and otherwise tools which should be restricted in
access due to licensing/etc.) were showing up in normal user's toolboxes
inside the workflow editor.
I feel that this is a bug, as the tool filters should be
This sounds like a bug; the primary toolbox and workflow editor toolbox
should reflect the same set of tools (exception being workflow-specific
control steps, etc). I've created a trello card to track this issue here:
https://trello.com/c/3TxFHkYR
That said, do note the warning on the dynamic
Okay, thanks for confirming and creating the card.
Yes...it's unfortunate that tool filters will not block tools entirely,
but this will get it out of the users' view in one more place.
On 12/17/2013 05:39 PM, Dannon Baker wrote:
This sounds like a bug; the primary toolbox and workflow editor
How do you have it set up on the main public galaxy install? I imagine that
people run enough big jobs that there there is enormous use of your shared
file system. How did you scale that to so many nodes without bogging down
the file system with large dataset transfers?
It seems that for now the
Agreed with Dannon, it is a bug that they are showing up in the workflow
editor but in general toolbox filters are not meant as a security mechanism.
You can block access to running specific tools (filtered or not) using
dynamic job destinations. (Under dynamic job destinations documentation (
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John,
I've been using the dynamic jobs and they've been working beautifully!
(For context, I wrote the initial revision of the Access Control page
based off of my readings and experiences setting it up in galaxy).
I, for one, would be in favour of
Hi,
the best start for using the API, that you found already, is the
documentation that, with a nice introduction, is nicely available here:
https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html
Regarding libraries your main controllers of interest are: *libraries*,
This does mostly make sense, and is very illuminating. I appreciate all the
help and I'm sorry that I'm so new to this.
I'm not sure I fully understand though. Do you mean that I could have a
main Galaxy install setup for the 200 nodes, for general purpose use with a
shared file system, and a
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