Hello everyone,
I have a question how to access the history name and tool number (the number
displayed in the history) in the XML tool definition file.
We want all tools of a history to log to a common log file using the tool
number to distinguish the different tools. Thus, I'd like to do
On Nov 4, 2011, at 8:03 PM, Chorny, Ilya wrote:
Looks like the mv is something I added and forgot about. I changed it to
shutil.copyfile and it works fine. This also has something to do with the
isilon. I pushed it to the actual user repository so you can check it out.
Okay, I'll have a
I am not sure what the copy is for. I did not add the move/copy I just changed
shutil.mv to os.system(mv) because it has less baggage. In fact if I comment
it out the upload still works.
Ilya
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Monday, November 07,
I pull the latest version of galaxy central and I still get this error when
clicking on published workflows. Any thoughts?
Error - type 'exceptions.TypeError': isinstance() arg 2 must be a class,
type, or tuple of classes and types and below.
Best,
Ilya
From:
Yep, I'm able to reproduce it now, should have a resolution shortly. Thanks!
On Nov 7, 2011, at 12:24 PM, Chorny, Ilya wrote:
Dannon,
I just cloned a fresh version of galaxy-central. I create a workflow using
just fastqc or groomer. I can run the work flow,etc. But when I publish it
Fixed in 0cdd7bb67d95, thanks for reporting the error.
-Dannon
On Nov 7, 2011, at 12:24 PM, Chorny, Ilya wrote:
Dannon,
I just cloned a fresh version of galaxy-central. I create a workflow using
just fastqc or groomer. I can run the work flow,etc. But when I publish it
and try to run it
I think there is another bug in the output selection of the workflows. If I
select only certain number of outputs (by selecting the orange star) to be show
in history following a workflow and then edit the workflow to show more
outputs, the number of outputs in the history does not change and
Greetings!
I would like to expose data I have in a relational database as a data
library in Galaxy. I would really like to do this without Galaxy having to
make a local copy of the data to the file system. Is this possible and
could you point me to any code examples and/or documentation?
I'm
Hello James,
This is not currently possible - the options for uploading files to Galaxy data
libraries is documented in our wiki at
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
On Nov 7, 2011, at 2:11 PM, James Ireland wrote:
Greetings!
I would like to
On Nov 4, 2011, at 1:11 PM, Carlos Borroto wrote:
Hi,
Reading a little more about this problem, I see Galaxy uses python
tempfile library (http://docs.python.org/library/tempfile.html),
specifically at line 70 in tools/samtools/sam_to_bam.py:
tmp_dir = tempfile.mkdtemp()
mkdtemp should
On Sep 29, 2011, at 11:02 PM, KOH Jia Yu Jayce wrote:
Hi
I’d like to enquire about the bug report. Apparently when someone sends a bug
report, everyone in the mailing list and the sender himself are supposed to
receive the bug report (as can be seen in the to field in the email sent
On Sep 30, 2011, at 9:32 AM, Iry Witham wrote:
When I run sh manage_db.sh upgrade I get the following error:
Hi Iry,
Sorry for missing this - were you ever able to resolve it?
Thanks,
--nate
2 - 3...
Traceback (most recent call last):
File ./scripts/manage_db.py, line 55, in module
On Oct 21, 2011, at 7:55 PM, Robert Day wrote:
Hi,
Sorry to bother you guys with such a simple thing. I'm quite new to the
terminal and command line etc. so downloading and getting Galaxy running on
my PC was a voyage of discovery! Anyhow, I have it, it's alive.. just
can't get
On Nov 2, 2011, at 4:48 PM, Arthur Goldberg wrote:
Hi
Where's the best documentation for parallel cluster support in Galaxy, please?
Hi Arthur,
Our documentation on running Galaxy as a production service, including on a
cluster, is available here:
http://usegalaxy.org/production
If
On Nov 2, 2011, at 4:45 PM, Oren Livne wrote:
Dear Nate,
My PYTHONPATH is already set to this value.
Hi Oren,
Is it exported? If it's set to Galaxy's lib directory, it should not be
possible that the galaxy module can't be found.
--nate
Best,
Oren
On Oct 27, 2011, at 8:23 AM, SHAUN WEBB wrote:
Hi, I updated my test server today and everything seemed fine. I added a new
library item via a URL. After that my history panel displays Internal Server
Error and I am getting the error below in paster.log:
Any ideas how this has occurred
On Oct 24, 2011, at 9:01 AM, Martin Dahlö wrote:
Hello there
As the subject hints, I am trying to export histories through the API.
Doing it through the web interface is a breeze, but has it been
implemented in the API yet? I could not find anything about it in the
examples or by searching
On Oct 25, 2011, at 2:43 AM, Andrew Warren wrote:
Hello,
I recently encountered a problem when trying to run Cufflinks on eight BAM
files on our galaxy instance (via the multi-input toggle) and received the
error: Unable to run job due to a misconfiguration of the Galaxy job running
Yan,
1. Right now, we host and you can use usegalaxy.org ( main.g2.bx.psu.edu ),
and test.bx.psu.edu. Main will be the most reliable server and what we
recommend you use, but test has a few beta tools that aren't available on main
yet. That said, test.g2.bx.psu.edu is very much for testing
Hi James,
Since genomic data files are often very large, Galaxy does not store them in a
database, so this specific scenario has not been implemented as far as I know.
However, you may be able to implement what you've described without too much
difficulty. If you could implement a layer on
Hello galaxy dev,
I have done some work on enabling multiple input files for multiple tool
parameters in a workflow. This could come in handy when running multiple
paired end data files for RNA Seq through a pipeline (I know this has been
discussed on a few different threads but I couldn't find
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