I have stumbled on some strange behaviour when uploading files to galaxy
via the upload.py tool. At times, the upload seems to be stalled in
history and is never actually performed, followed by a seemingly
infinite history update (see log below). My system is Ubuntu 11.10 and
Hello everybody :)
Today, I have a question related to timeout management in Galaxy.
More particularly, I'm searching for a way to set (in a configuration
file if possible) all timeouts related to DRMAA and timeouts related to
communication between Galaxy and SGE.
My goal is to increase
Galaxy Sample Tracking is not supported by the core Galaxy development team, so
you're on your own on this one. I'm told the problem is that the format of the
library content ID has been changed in the API, so the script needs to be
updated to reflect that. Sorry for the
I guess we see similar things: a new history item is created, it turns
purple, stays like this apparently forever while no job id is created
(ie I don't see the job in any of the report tools).
To be honest we ignore them, because:
a) it only (as far as I can tell) happens with big data
We get the behavior mentioned some times too, its not reproducible
just like you mentioned. Some times it happens with small files, some
times with large files and again as you said it doesn't happen all the
Now I haven't seen this yet on our Galaxy dev server which is the
I haven't been patient enough to wait really long, but I can give that a
As Leandro mentioned, I've also seen it in kilobyte to megabyte sized
files. My Galaxy is forked from the latest galaxy-dist.
On 02/22/2012 04:47 PM, Leandro Hermida wrote:
Huh? I have many string inputs to some particular workflow steps...Those are parameters etc that need to be entered or chosen from a dropdown..How would we deal with those kinds of entries into a workflow in the API? Or do all of them have to be pre-set?ThanksThonOn Feb 21, 2012, at 04:21 PM,
Ahh, I see what you're asking. I thought you were referring to providing dataset inputs by name, my mistake.Currently running workflows through the API doesn't support defining inputs other than datasets, that is, it expects workflows to be fully pre-defined with nothing 'set at runtime' other
On Thu, Feb 16, 2012 at 9:02 PM, Peter wrote:
On Thu, Feb 16, 2012 at 6:42 PM, Chris wrote:
On Feb 16, 2012, at 12:24 PM, Peter wrote:
I also need to look at merging multiple BLAST XML outputs,
but this is looking promising.
Yep, that's definitely one where a simple concatenation
Awesome, I'll take a look. And, if you're able to pull it together easily enough, clean branches are always nice.-DannonOn Feb 22, 2012, at 10:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Basic BLAST XML merging implemented and apparently working:
This tool is from the Tool Shed and is maintained by the tool author. To
contact them about functionality or problems, go to the Tool Shed at
http://toolshed.g2.bx.psu.edu/, locate the repository (search by
'snpEff'), click on the name, in the the top far right corner locate the
I am going to send your question over to the galaxy-...@bx.psu.edu
mailing list so that the development community can offer feedback.
Th galaxy-user list is primarily for
When I click on Admin-'Search and browse tool sheds'-'Galaxy main tool shed',
it shows the first page of Valid repositories. However, clicking '2', '3',
'4', or 'Show All' has no effect. I can only display the first page of
However, if I search for valid tools using the menu
On Tue, Feb 21, 2012 at 5:49 PM, Borrone, James
I am trying to use the FastX tools on the Main server to trim and manipulate
FASTQ files extracted directly from an sff file (again using the main galaxy
web server). In using Clip and the Reverse
I cannot reproduce this behavior from my local Galaxy instance, but clicking
'2', '3', '4' or 'Show All does take a second or more to display the response.
Can you provide more information about the environment you have or what you
are doing to reproduce this?
What browser / version are you using?
On Feb 22, 2012, at 4:18 PM, David Hoover wrote:
It's a local install, hg summary gives 6621:26920e20157f. I'm using MySQL as
a backend database and have the following options set to non-default:
port = 8081
host = 0.0.0.0
Bjoern is correct. A few other choices are:
We send out a tweet when new tools are added. This isn't automatic, or
necessarily for all tools, but something we plan on continuing. If
interested, you could follow us on twitter or track the Twitter wiki:
That is a wonderful news and I am eager to see it in tool shed. I am
going to check tool shed frequently these days to get it asap.
On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS vipin...@gmail.com wrote:
We have the recent release version of DESeq at our Galaxy instance,
In case you aren't aware, you can set your user preferences for your account in
the tool shed to receive an email message when a new repository's first upload
occurs. This would keep you from having to check the tool shed. Go to User -
Preferences - Manage your email alerts and you'll
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