Hi, I've redirected all of my outputs in an other directory with my own
names after each run of tools..
But when the users want to rename their datasets on the history, I would
want that this change occurs on my output files already register in the
computer.
So where can I find the xml file of
Dear all,
I have an today up-to-date galaxy-dist running (7986:12fcd068b12e). All seems
to work fine.
However in the admin panel when I make a quotum it works unless I let it make
default at the same time or allocate groups of users to the quota.
Just creating the quotem works fine without any
Hi Matthiew,
Can you clarify the version of Galaxy you are using? What is the result of
typing hg heads in your Galaxy installation directory?
ALso, I noticed the following in your paster log:
131.254.16.26 - - [12/Nov/2012:10:52:26 +0200] GET
Hi All,
Due to previous DB errors we decided to let galaxy-dist repopulate the database
(MySQL). We purged all tables from the DB and when restarting galaxy it
repopulates the DB on the fly while doing all migration steps. A nicely running
galaxy as the result.
I encountered a strange error
The general case is hard and it was brought up repeatedly at the
Galaxy community conference. One path might be this work
(https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-datatypes)
on defining datasets that represent homongenous collections of files,
but there are no easy
From IRC (weeks ago):
(03:15:01 PM) jmchilton: Ideally, what would the API uri for assigning
a tag to a histories dataset be? POST to
api/tags/tag_name/item_class(e.g.
HistoryDatasetAssociation)/encoded_id or POST to
api/histories/history_id/contents/dataset_id/tags/tag_name or
POST to
Dear list,
I would like to start using Amazon's spot pricing model for my
Galaxy/Cloudman instances (e.g. an on demand master node with spot instance
worker nodes). However, this means that Amazon at times of spot prices
higher than my set price limit will shutdown my instances without notion.
I
On Nov 12, 2012, at 10:23 AM, Jorrit Boekel jorrit.boe...@scilifelab.se wrote:
I was therefore looking for fault tolerance mechanisms in the galaxy project,
which I seem to remember existed. Somehow I can't find anything about it
right now though.
I've tested a little bit, and it seems
Ah, sorry I missed this.
From IRC (weeks ago):
(03:15:01 PM) jmchilton: Ideally, what would the API uri for assigning
a tag to a histories dataset be? POST to
api/tags/tag_name/item_class(e.g.
HistoryDatasetAssociation)/encoded_id or POST to
On Mon, Nov 12, 2012 at 9:43 AM, John Chilton chil...@msi.umn.edu wrote:
From IRC (weeks ago):
(03:15:01 PM) jmchilton: Ideally, what would the API uri for assigning
a tag to a histories dataset be? POST to
api/tags/tag_name/item_class(e.g.
HistoryDatasetAssociation)/encoded_id or POST to
On Nov 6, 2012, at 2:44 PM, Alan V. Cowles wrote:
same error without the symlink, this time with actual syntax:
galaxy.jobs ERROR 2012-11-06 14:41:06,596 (11) Failed to change ownership of
/usr/local/galaxy/galaxy-dist/database/job_working_directory/000/11, failing
Hi Alan,
You're using
On Nov 7, 2012, at 9:37 PM, Rolando Mantilla wrote:
hello guys I'm kinda new using galaxy but I'm having an issue I tried to run
my workflow and it just stopped, I was able to load both of the sequences but
I could not run the whole workflow. I do have enable_job_execution=True, so I
don't
On Nov 8, 2012, at 8:55 PM, Liisa Koski wrote:
Hi Nate,
I'm back to trying to figure this out again as I am running out of disk
space. I added the bit of code you suggested below, but I don't think it
helped, I'm not so familiar with python.
I'm now running Galaxy Reports and it tells
On Nov 9, 2012, at 9:24 AM, greg wrote:
I see this setting in the universe_wsgi.ini file:
# Temporary files are stored in this directory.
new_file_path = /scratch/galaxy
Is this only used by the web server or will job runners pick up this
setting and use it for temp files?
I'm also
Hi, guys,
I noticed that set_metadata.sh is not in the tools folder as other tools.
Can I set a tool runner for set_metadata.sh so that I can use specific
resources (like specific compute node in the cluster) to run
set_metadata.sh?
Thanks,
Luobin
While we're talking about the tags API, I'd also like to see if we can
think about the annotations API.
Can it be formulated in the same manner as the proposal for the tags api?
Kyle
On Mon, Nov 12, 2012 at 7:49 AM, James Taylor ja...@jamestaylor.org wrote:
On Mon, Nov 12, 2012 at 9:43 AM, John
While we're talking about the tags API, I'd also like to see if we can
think about the annotations API.
Can it be formulated in the same manner as the proposal for the tags api?
Yes, annotations and tags share the same structure, so it makes sense that the
tag API structure can be used for
Dear galaxy developers--
I'd like to bring your attention to the call for participation included below
this message. A Phylotastic system is a distributed tree-of-life delivery
system composed of web services. Although it is not readily apparent from the
presentation linked below, the
Hi Greg !
Thanks for the quick answer.
I am using the 7720 parent version but I keep it up-to-date without any
problems.
Enclosed you'll find the 'paster.log' file generated when I start Galaxy and
try to access the manage installed tool shed repositories page.
Cheers,
Mathieu Bahin
That did it! Thanks Nate!
From: Nate Coraor n...@bx.psu.edu
To: Liisa Koski liisa.ko...@basf.com
Cc: galaxy-dev@lists.bx.psu.edu
Date: 12/11/2012 12:13 PM
Subject:Re: [galaxy-dev] Error when running cleanup_datasets.py
On Nov 8, 2012, at 8:55 PM, Liisa Koski wrote:
Hi
On Nov 12, 2012, at 5:38 AM, Bossers, Alex wrote:
Dear all,
I have an today up-to-date galaxy-dist running (7986:12fcd068b12e). All seems
to work fine.
However in the admin panel when I make a quotum it works unless I let it make
default at the same time or allocate groups of users to
On Nov 12, 2012, at 11:17 AM, Alan V. Cowles wrote:
yeah I'm not seeing the folder 11, I have a folder 2 created july 19...
(galaxy_env)-bash-4.1$ pwd
/usr/local/galaxy/galaxy-dist/database/job_working_directory/000
(galaxy_env)-bash-4.1$ ls -al
total 12
drwxrwxr-x 3 galaxy galaxy
On Nov 12, 2012, at 12:38 PM, Luobin Yang wrote:
Hi, guys,
I noticed that set_metadata.sh is not in the tools folder as other tools. Can
I set a tool runner for set_metadata.sh so that I can use specific resources
(like specific compute node in the cluster) to run set_metadata.sh?
Hi
Nate,
crapthat fixed it...not sure why that setting didn't show up in the svn
diff but anyway...it's working again.
I wonder; if a user is member of two groups with different quota...will the
largest be effective?
Thanks
Alex
Van: Nate Coraor
On Nov 12, 2012, at 2:35 PM, Bossers, Alex wrote:
Nate,
crapthat fixed it...not sure why that setting didn't show up in the svn
diff but anyway...it's working again.
I wonder; if a user is member of two groups with different quota...will the
largest be effective?
It's been a while
Hi Mathieu,
It's pretty difficult to tell you where to start looking within your
environment for the cause of the problem.
You mentioned that you attempted to uninstall the repository name mothur from
you local Galaxy instance, and that action produced this problem. What is the
result of
Hi Kevin,
I'm not clear why you want to create a dummy env.sh file, so I may not be
able to answer your question. However, see the following tool shed wiki page
in case you want to create an env.sh file that is sourced when the tool(s)
included in the installed repository is executed in the
Hi, Nate,
Thanks for reply. Is it a standalone job that's dispatched when the edit
attribute page is saved?
Thanks,
Luobin
On Mon, Nov 12, 2012 at 12:23 PM, Nate Coraor n...@bx.psu.edu wrote:
On Nov 12, 2012, at 12:38 PM, Luobin Yang wrote:
Hi, guys,
I noticed that set_metadata.sh is
Hi Peter,
I've tweaked the template for this email in change set 8211:3024a86c0d0d, which
is currently running on the test tool shed. It'll be moved to the main tool
shed 2 Galaxy releases from now - I'm not quite sure of the date of that
release.
Thanks for requesting this fix.
Greg Von
On Mon, Nov 12, 2012 at 9:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
I've tweaked the template for this email in change set 8211:3024a86c0d0d,
which is currently running on the test tool shed. It'll be moved to the main
tool shed 2 Galaxy releases from now - I'm not quite sure
Essentially, this the similar to a dataset upload where the origin is from a
web page when a user clicks on a HTML button. The button is not part of the
tool framework but any number of possible
I am writing a variety of data editors in JavaScript and it would be convenient
to upload the
Hi Greg,
I am wondering the similar thing. If I understand Kevin's post correctly, I
think the question really is: if the automated tools build is
the requirement for creating the shed tool version specific env.sh
automatically during the shed tool installation.
Take BWA on the Tool Shed as an
What is the error that you're seeing on the server side?
I haven't tried this myself, but Brad Chapman suggested this example payload:
--
{tool_id: upload1,
history_id: identifier of history to use,
params: {file_type: vcf,
dbkey: hg19,
files_0|url_paste:
Hi All,
That's the idea.
An env.sh for each toolshed tool (or tool dependency). Everything is
generic and modular this way, while giving us better control over
versions, and control over compilation settings.
Here is something I've tried.
install version=1.0
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