From: Eli Reuveni
Sent: Monday, April 16, 2012 9:13 AM
To: 'galaxy-dev@lists.bx.psu.edu'
Subject: where can I find galaxy code documentation?
Hi,
I have a local galaxy instance in my institute and have few basic questions:
1) I need to enable galaxy to upload large files from the local
Hi dev-list,
I have noticed, that when I clone a workflow, the new workflow
apparently inherits all tags from all my workflows or something similar.
The result is that when ever I clone a workflow the number of tags in
the tag list doubles, and thus rapidly grows towards infinity, and
I love the improvements you recently made to the web interface layout in
galaxy-central, it's really neat! Collapsing the margins and making
everything smoother makes the interface really easier to read.
Thanks for the hard work, as always,
L-A
On Mon, Apr 16, 2012 at 8:12 AM, Frank Sørensen frank.soren...@ki.au.dk wrote:
Hi dev-list,
I have noticed, that when I clone a workflow, the new workflow apparently
inherits all tags from all my workflows or something similar. The result is
that when ever I clone a workflow the number of
Hi Peter,
Thanks for the prompt answer.
I'm not quite sure which release I'm running. But I'll try to update and
see if the problem is solved.
Kind Regards
Frank
Den 16-04-2012 09:54, Peter Cock skrev:
On Mon, Apr 16, 2012 at 8:12 AM, Frank Sørensenfrank.soren...@ki.au.dk wrote:
Hi
Hi,
I am getting the error This link may not be followed from within Galaxy. When
I try to upload a data file to my local galaxy.
I have traced back the error to root.py (RootController class).
Could anyone help me with that?
Best
___
Hi Amanda,
I'll need to see your paster log to be able to help on this one. You can view
it using tail -f community_webapp.log (without the quotes) from your Galaxy
install directory. Can you respond back with the content?
Thanks,
Greg Von Kuster
On Apr 8, 2012, at 1:58 PM, Amanda Zuzolo
Hi
We are in the process of migrating our Galaxy servers to the current
March 12, 2012 release ('6799:40f1816d6857').
We have encountered two issues, which I guess are related:
If I restart the server, I get:
galaxy.model.migrate.check INFO 2012-04-16 09:24:50,391 At database
version 93
Hi Rob,
When you import a workflow into a Galaxy instance, the instance must have all
tools required by the workflow available in its tool panel. I've only seen
this error when the workflow requires a tool that is not available, so can you
let us know if this is the case?
Thanks,
Greg Von
Hello all,
Just a reminder that the abstract submission deadline for the 2012 Galaxy
Community Conference (GCC2012) is TODAY. See
http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts for details.
Thanks,
Dave C
On Mon, Apr 9, 2012 at 2:03 PM, Dave Clements cleme...@galaxyproject.orgwrote:
Thanks for the example, Frank.
You can upload to data libraries directly from the local filesystem. The
relevant documentation is here:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Eli, with respect to the question about modifying galaxy-dist/lib:
On Apr 16, 2012, at 7:13 AM, Eli Reuveni wrote:
Hi,
I am getting the error “This link may not be followed from within Galaxy.”
When I try to upload a data file to my local galaxy.
I have traced back the error to root.py (RootController class).
Could anyone help me with that?
Hi
Hello,
I've integrated a tool into my Galaxy instance, but when I run the tool I get
this error:
galaxy.objectstore CRITICAL 2012-04-16 11:25:56,697 Error copying
/home/galaxy/galaxy-dist/database/job_working_directory/000/307/dataset_431_files/unweighted_unifrac_2d_continuous
to
Hi All,
I was trying to setup the Galaxy tool dependencies, and I met the following
problem when running sam-to-bam in samtools:
Traceback (most recent call last):
File /mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py,
line 336, in finish_job
Hi Robert,
I've cc'd the galaxy-dev list on this reply since the workflow components are
primarily supported by other Galaxy development team members and I'm not
optimally suited to handle this issue. Please keep responses on the galaxy-dev
mail list so others that are interested can follow
Hi everybody,
I was searching through the Galaxy code and I find the solution: the function
responsible for copying files is using shutil.copy function, which only allows
copy files. I've modified this function to use shutil.copytree in case of
file_name is a directory. I can send you the code
Robert,
It sounds like you're experiencing two separate problems to me. Let's
isolating the problem to just the FastQC tool install, first, and move on from
there. There is a FastQC tool in your toolbar, and execution results in the
error you describe in the previous email of 'Fastq failed.
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