I'm assuming you're referring to main.g2.bx.psu.edu's tool configuration as
a reference. Some of these components are installed via the tool shed, and
others may have been manually added to main and are not included in the
base tool_conf.xml.sample. I may be able to point you in the right
28, 2013 at 12:42 PM, Dannon Baker dannon.ba...@gmail.comwrote:
I'm assuming you're referring to main.g2.bx.psu.edu's tool configuration
as a reference. Some of these components are installed via the tool shed,
and others may have been manually added to main and are not included in the
base
: Wednesday, 29 May 2013 2:45 PM
To: galaxy-dev@lists.bx.psu.edu; 'Dannon Baker'; 'robert.lecl...@gmail.com
'
Subject: Re: Creating multiple datasets in a libset
Hi Guys,
Did you manage to get multiple datasets working? I can't seem to
upload multiple files. Only the last file appears
As long as you're able to execute your php script from the command line, it
should work fine.
-Dannon
On Wed, May 29, 2013 at 7:25 AM, Prasun Dutta prasundutt...@yahoo.co.inwrote:
Hi,
If I have some programs in php which I need to integrate in Galaxy as a
tool, can I do it? I know if I
.
-Nick
On Tue, May 28, 2013 at 3:58 PM, Dannon Baker dannon.ba...@gmail.comwrote:
Hi Nick,
Not sure I completely understand what you're trying to do here. So, you
want to have a galaxy head node on AWS that dispatches jobs to a non-AWS
private SGE cluster?
-Dannon
On Thu, May 16
No firm release set for the new cloudman yet, but you can always follow
development here:
https://trello.com/board/galaxy-cloudman/5136209e9beefacb77004e6d
There are a few final issues we're wrapping up before we can release, but
we're hoping it'll be soon.
On Fri, May 31, 2013 at 7:31 AM,
On Fri, May 31, 2013 at 9:51 AM, John Chilton chil...@msi.umn.edu wrote:
Could you enable comments for non-board members like the Galaxy
Development Trello allows?
Of course, actually thought I'd already done that. Fixed!
___
Please
Hi Linda,
The decorator issue should be resolved in galaxy-central now. I'm setting
up a test environment to see if I can reproduce the mysql issue now, and
will let you know what I come up with.
Thanks!
-Dannon
On Wed, Jun 5, 2013 at 11:12 AM, Linda Cham lc...@us.ibm.com wrote:
Hi. I am
Thanks for the bug fix, (and for the reminder that it was still sitting in
the inbox, sorry about that). I've verified the fix as well and pulled it
into -central.
-Dannon
On Thu, Jun 6, 2013 at 10:13 AM, Lance Parsons lpars...@princeton.eduwrote:
Thanks for confirmation Björn.
Pull
...@soe.ucsc.eduwrote:
Hi Dannon,
I deleted the declaration to select2 in base.mako (line 42) and that fixed
the problem for now. (thanks to Ted for the tip!)
-Robert
On Jun 4, 2013, at 1:30 PM, Dannon Baker wrote:
Hey Robert,
Thanks for catching this; I'm working on getting a fix out (this affects
How did you install your python, or are you using the default ubuntu 12.04
version? The bz2 module should be distributed with any python since 2.3.
-Dannon
On Thu, Jun 6, 2013 at 3:25 PM, Andrew Krohn alk...@nau.edu wrote:
I looked through others' problems, but this seems unique. I just did
-for-python-2-7-2
On Thu, Jun 6, 2013 at 4:19 PM, Andrew Krohn alk...@nau.edu wrote:
I am using the default ubuntu 12.04 python.
Andrew Krohn
PhD Candidate, NAU Biological Sciences
Research Technician, EnGGen
On Thu, Jun 6, 2013 at 1:17 PM, Dannon Baker dannon.ba...@gmail.comwrote:
How did
,
From: Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de
To: Linda Cham/Poughkeepsie/IBM@IBMUS
Cc: Dannon Baker dannon.ba...@gmail.com, Galaxy Dev
galaxy-dev@lists.bx.psu.edu
Date: 06/05/2013 04:30 PM
Subject: Re: [galaxy-dev] Installation of 20130603 Galaxy image with
MySQL fails
, at 10:42 AM, Dannon Baker wrote:
That'll work, but it'll deactivate select2 across the board for all pages
in your galaxy instance. I committed a fix for those specific admin pages
yesterday, available in galaxy-central (stable as well as default branch).
-Dannon
On Thu, Jun 6, 2013 at 1
Even though the dialect name changed, the existing database urls should be
compatible (postgres:///...). Did you find this not to be the case?
-Dannon
On Mon, Jun 10, 2013 at 12:54 PM, Richard Burhans r...@bx.psu.edu wrote:
The SQLAlchemy postgres dialect was renamed to postgresql.
Christophe,
Glad it's working. The updates should merge seamlessly so you shouldn't
need to do anything else when you update again. That said, for future use,
you can swap branches like: 'hg update stable' to swap to the stable
branch. If you're on galaxy-dist, you can still pull (and update)
Hi Vipin,
There isn't currently a page export/import mechanism and the steps outlined
above seem reasonable. Of course, contributions are appreciated should
anyone wish to undertake this project.
-Dannon
On Thu, Jun 13, 2013 at 5:27 PM, Vipin TS vipin...@gmail.com wrote:
Hello dev-team,
The web process is definitely the bottleneck right now, creating more
should improve things. I'd guess it wouldn't speed up any individual
submission, but it'd allow you to submit several at once. Lastly, this is
a known issue that we're hoping to resolve with a rewrite of the workflow
If you're starting a bunch of new clusters at once, I'd look into using the
Share-an-instance functionality to create a single base configuration
with the volume size you prefer. This would allow you to have a predefined
volume (with a specific size) that starts automatically. The share_string
The error ERROR: could not read block 326 in file base/257536/259291:
read only 0 of 8192 bytes line makes me wonder if your database may have
been corrupt prior to the upgrade/dump. Some brief googling suggests that
this could be hardware failure induced among other things. Can you check
the
This is actually a bug in the current tip of galaxy-central that we should
have resolved shortly. We should have an update out today, or you can
downgrade your galaxy to revision dfba9b0 (hg update -r dfba9b0).
-Dannon
On Tue, Jun 18, 2013 at 8:12 AM, Marco Ocana
This should now be resolved in -central. If you update again, you'll get
the changes and your instance should work fine.
-Dannon
On Tue, Jun 18, 2013 at 8:34 AM, Dannon Baker dannon.ba...@gmail.comwrote:
This is actually a bug in the current tip of galaxy-central that we should
have
On Tue, Jun 18, 2013 at 10:54 AM, Sebastian Schaaf
sch...@ibe.med.uni-muenchen.de wrote:
Thus, the cloning process as the LDAP user (did not want to store the
foreign username/password explicitly in the galaxy user files) worked,
although I get this message:
*** failed to import extension
20130603.
In the thread of her mail Dannon Baker said :
That said, this doesn't resolve the mysql index issues, which I'm
currently working on. I hope to have a fix for them available soon,
though.
I would like to know if what is the status of this thread. Should I use
the solution provided
Hsiong,
Could you try 'hg clone --verbose --debug
https://bitbucket.org/galaxy/galaxy-dist/' to see if we get more useful
error output? If it passed the warning and went ahead and got all the
changes then I'm not sure if that's an issue.
Also, I'm swapping this thread to the galaxy-dev list,
It's that previous versions of sqlalchemy-migrate didn't clean up these tables
under sqlite and didn't mind overwriting them if they existed, but the new
version both does clean up after itself, and expects the table to not exist,
failing miserably if it does.
I think there's a Trello card for
On Mon, Jul 1, 2013 at 8:34 PM, Brad Chapman chapm...@50mail.com wrote:
This was a typo in the downgrade function for one of the patches. I
pushed a fix so if you update from bitbucket things should work smoothly
again (once we get to problem 2 below).
For anyone with galaxy-dist commit
Hey Mo,
The new volume we pushed out for the conference has several known issues.
Enis and I are both away from the office on travel right now, but updating
the volume and fixing these issues is the first thing I'll be doing when
I'm back next week.
For now, you can launch using the
Can you verify that the volume does still exist in your account, and that
you're launching from the same availability zone that the volume exists in?
On Mon, Jul 22, 2013 at 4:13 PM, Ravpreet Setia
ravpreet.se...@oicr.on.cawrote:
- This is what has been reported by the cluster status log:
Yes, you can still use the deprecated AMIs. What error are you seeing when
you try to ssh in?
On Mon, Jul 22, 2013 at 4:30 PM, Ravpreet Setia
ravpreet.se...@oicr.on.cawrote:
I tried launching an instance specifying ami-da58aab3 as the AMI but I
am unable to SSH or access Cloudman using the
The warning message printed by the first ssh attempt indicates that you
have no cloudman_key_pair.pem in the directory you executed the ssh command
from. Find this file (or create a new one) and you'll be able to ssh.
Good luck, and please keep threads on the list instead of emailing
directly.
The best contact address for these kinds of issues is galaxy-b...@bx.psu.edu
.
There was a brief delay with some jobs running, but everything should be
working fine now.
-Dannon
On Wed, Jul 24, 2013 at 5:30 AM, Ali Sharifi Zarchi ashari...@gmail.comwrote:
Hi everybody
Since yesterday all
On Thu, Jul 25, 2013 at 4:47 PM, Deniz Erezyilmaz deniz...@gmail.comwrote:
The workaround doesn't seem to work
Can you tell me what happens when you launch with the workaround mentioned
previously (
https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop)?
This
suddenly Saturday June 29, when the share string would not load. Thanks
again, Deniz
On Thu, Jul 25, 2013 at 5:19 PM, Dannon Baker dannon.ba...@gmail.comwrote:
On Thu, Jul 25, 2013 at 4:47 PM, Deniz Erezyilmaz deniz...@gmail.comwrote:
The workaround doesn't seem to work
Can you tell me
What is the problem you're observing, and do you see any errors in the
galaxy log or javascript console?
-Dannon
On Mon, Jul 29, 2013 at 5:51 AM, Misharl mon mish...@hotmail.com wrote:
Hi everybody,
In my lab, after upgrading our Galaxy instance to the latest version, we
have a problem
What happens when you attempt view the tabular file? Does it automatically
download instead of displaying, for example?
On Mon, Jul 29, 2013 at 9:54 AM, Misharl mon mish...@hotmail.com wrote:
Hi Dannon,
Thank you very much for replying. The problem is that we cannot display
any tabular
We're working on it but don't have a specific ETA for the release of the
new volume. For now, you can continue to create and run non-migrated
clusters using the previous version of Cloudman using this launch form:
https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop
...@gmail.comwrote:
HI - did you find anything with the share string? Thanks, Deniz
On Fri, Jul 26, 2013 at 3:32 PM, Dannon Baker dannon.ba...@gmail.comwrote:
Ahh, ok, I misunderstood and thought you were saying there was a
different error for the workaround. Are you able to send me the share
string
It shouldn't, unless the root cause of that error also affected the FTP
transfer. Does FileZilla say there are any transmission errors?
On Thu, Aug 1, 2013 at 1:16 AM, Mark Edward Fabreag merfabr...@gmail.comwrote:
Good day!
While I was uploading the file (through FileZilla), I encountered
:* Thursday, August 01, 2013 4:11 PM
*To:* Dannon Baker
*Cc:* galaxy-dev@lists.bx.psu.edu
*Subject:* Re: [galaxy-dev] Cloudman - When will the symlinks be resolved
?
Here it is:
'pd.yaml' not found at paths.py load!
Set paths.P_GALAXY_HOME as '/mnt/galaxyTools/galaxy-central'
Python
Hi Boaz,
You should be able to edit universe_wsgi.ini (line ~30) to specify any port
you'd like -- so simply pick something other than 8080, save the file, and
retry. Remember to remove the hash (#) at the beginning of the line to
have it take effect.
-Dannon
On Mon, Aug 5, 2013 at 12:42 PM,
A new tools volume will be released shortly. For now, you can launch the
previous cloudman release using the following:
https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop
On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly
ulyanov_anat...@allergan.com wrote:
...@oicr.on.cawrote:
Anatoly, did this method work for you? It is not working for me.
--
*From:* galaxy-dev-boun...@lists.bx.psu.edu [
galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Dannon Baker [
dannon.ba...@gmail.com]
*Sent:* Wednesday, August 07, 2013 8:00 PM
On Thu, Aug 8, 2013 at 4:57 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote:
Yeah, nothing happens after SGE gets to the running state. The directory
structure of the old ami does not appear in /mnt. The log was posted in the
following thread:
Ahh, ok - I assumed since there was no
This looks to be a guppy bug that has now been fixed (
http://sourceforge.net/p/guppy-pe/bugs/10/) so we'll update the egg from
our end, thanks!
For now, you can either build your own guppy 0.1.9+ egg to fix it or
disable use_memdump in your universe (to skip it completely). Unless
you're
Peter,
Thanks for noticing this -- the text in the UI should definitely reflect
which output it's referring to. Hide output_pos, etc.
https://trello.com/c/KAtwLSiV/1069-workflow-actions-cosmetic-issues
-Dannon
On Wed, Aug 21, 2013 at 7:16 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
Hi
Hey Peter,
I've reproduced this here, thanks. Unfortunately this got missed
previously, once we had the import itself working. To be clear, though,
the workflow itself is still completely functional, imports and runs, and
the only issue is the inability to view the svg?
I think what's causing
Quick followup on this one -- had you manually tweaked this workflow prior
to upload? I see all of the tool identifiers are the short form 'signalp3'
and not the long-form toolshed included versions.
On Wed, Aug 21, 2013 at 8:25 AM, Dannon Baker dannon.ba...@gmail.comwrote:
Hey Peter,
I've
On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
Via the Tool Shed I couldn't see the import workflow action... from
memory it was on the broken SVG page?
Yep, that's where it was.
These are not tweaked - it is an old workflow created with manually
installed tools
are in the toolshed, this sort of thing
shouldn't crop up because you'll have the correct version available.
I've committed a temporary fix in 10423:3c60f6a7dedc.
On Wed, Aug 21, 2013 at 9:14 AM, Dannon Baker dannon.ba...@gmail.comwrote:
On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock p.j.a.c
Hi Alistair,
One major goal of the Galaxy cloud offering is that it works out of the box
with a very large selection of tools and indices installed and ready to go,
with no configuration necessary. My workshop heuristic is two students per
node using regular m1.xlarge nodes (though input from
Can you get a dump of table sizes for us to compare with?
http://wiki.postgresql.org/wiki/Disk_Usage
On Thu, Aug 29, 2013 at 12:05 PM, Nate Coraor n...@bx.psu.edu wrote:
On Aug 29, 2013, at 11:50 AM, Nate Coraor wrote:
On Aug 26, 2013, at 5:03 AM, Christophe Antoniewski wrote:
Hi
The iRods integration is under active development, follow progress here:
https://trello.com/c/Sp9XvRfD/1072-object-store-write-an-irods-plugin.
-Dannon
On Thu, Sep 5, 2013 at 11:27 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote:
Hi All, Is there any update on iRods integration in galaxy ? One
On Thu, Sep 5, 2013 at 5:31 PM, Dannon Baker dannon.ba...@gmail.comwrote:
The iRods integration is under active development, follow progress here:
https://trello.com/c/Sp9XvRfD/1072-object-store-write-an-irods-plugin.
-Dannon
On Thu, Sep 5, 2013 at 11:27 AM, Zeeshan Ali Shah zas
Eric,
What version of posgresql are you using? The script has a comment that
indicates you need 9.1+ (and I'm using 9.1.9), and it works out of the box
for me.
-Dannon
On Fri, Sep 20, 2013 at 7:35 AM, Eric Kuyt eric.ku...@wur.nl wrote:
Hi All,
I'm trying to do some cleanup in my test
Are you using Input Dataset steps in your workflows? The multiple inputs
feature uses these to know how to distribute inputs -- other than that no
other configuration steps are necessary.
On Tue, Sep 24, 2013 at 2:43 PM, Adam Brenner aebre...@uci.edu wrote:
Howdy,
On our local galaxy
This looks to be a bug with the version of babel we're using (fixed in a
newer revision that I'll update to after testing), combined with improperly
set environment variables. Can you check your environment (just `env` in a
terminal) and look for LC_ALL, LANGUAGE, and LANG. Are any of these set
Nothing formal. The .ga extension is simply the workflow dictionary
exported as .json, if that helps -- there's no extra magic to the format.
You may want to look at the workflow API, some users have had success
integrating workflows created on the fly using it.
-Dannon
On Mon, Oct 7, 2013 at
a new workflow. I will dig and see if anyone has published or
presented on their internal libraries that create workflows on the fly.
Thanks
Takadonet
On Mon, Oct 7, 2013 at 11:18 AM, Dannon Baker dannon.ba...@gmail.comwrote:
Nothing formal. The .ga extension is simply the workflow
On Tue, Oct 8, 2013 at 4:48 AM, Ryota Yamanaka
yaman...@genome.rcast.u-tokyo.ac.jp wrote:
1) Do you plan to clone CloudMan AMI to other regions outside the US
in the near future?
2) Or, is there any way we can build CloudMan in such regions, with or
without your support?
Yes, we do plan on
Whoever your organization administrator is will need to either create those
keys for you, or allow your IAM user access to them. Are you able to
contact the person that administers your account?
On Tue, Oct 29, 2013 at 10:52 AM, Manisha Sapre msa...@nmdp.org wrote:
Good Morning Dannon
we
msa...@nmdp.org wrote:
Yes , all users have been allotted a private key , this error is after
ssh-add ( private key),
From: Dannon Baker dannon.ba...@gmail.com
Date: Tuesday, October 29, 2013 10:15 AM
To: System Administrator msa...@nmdp.org
Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev
this be a problem with root access ? Thanks
From: Dannon Baker dannon.ba...@gmail.com
Date: Tuesday, October 29, 2013 10:25 AM
To: System Administrator msa...@nmdp.org
Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu, David
Roe d...@nmdp.org
Subject: Re: [galaxy-dev] cloning Galaxy
Hi Pieter,
We've worked out what we think is the right way to solve this for Galaxy
and expect work to start soon. See the trello card (
https://trello.com/c/325AXIEr/613-tools-dataset-collections) for more
details.
For your particular tool, the first workaround that comes to mind would be
A short term option that just occurred to me would be to run a sort of
post-job-action for output datasets, deleting any non-output non-necessary
(anymore) intermediate parents.
On Wed, Nov 13, 2013 at 11:59 AM, John Chilton chil...@msi.umn.edu wrote:
On Wed, Nov 13, 2013 at 10:34 AM, Peter
This may be due to an incorrect reference to '/mnt/galaxyTools' in the
galaxy user's .sge_request file.
If you're comfortable with ssh and editing files on the server, you can log
in and edit the file (the path should be /mnt/galaxy instead), and you
should be good to go. Feel free to reply
I believe subsequent jobs should use the new paths automatically, yes.
On Mon, Nov 18, 2013 at 12:14 PM, Young, Lynn (NIH/OD/ORS) [E]
ly...@mail.nih.gov wrote:
Hi Dannon,
I edited the file.
Will the system automatically recognize the change?
Warmly,
Lynn
From: Dannon Baker dannon.ba
Hi,
That sort of sharing only works within a single galaxy instance; users are
not shared between different galaxies. To copy an entire history from one
instance to another you will want to use the history export/import
functionality. History context menu - Export to file on the source
of sharing data, cloud amazon charges
$0.120
per GB data transfer, is there a work around ?
also does that mean a worker node cannot communicate with master instance
directly and use same below protocol to share history ?
Thanks
msapre
From: Dannon Baker dannon.ba...@gmail.com
Date: Tuesday
On Wed, Nov 20, 2013 at 9:07 AM, Manisha Sapre msa...@nmdp.org wrote:
apologies if the second question was not framed properly, but it seems
there is a fee to share output datasets between nodes on same master
instance ?
No.
___
Please
On Tue, Dec 3, 2013 at 5:49 AM, Bjoern Gruening
bjoern.gruen...@gmail.comwrote:
The new discs will be type=distributed id=primary and the old disc
will become type=disk id=secondary. If I understood correctly the
old disc is them in some read-only state and will not touched until the
primary
If you wanted to implement fancier tiling and display for tiff, the
extension point for this would be in the datatype's display_data method.
You can use this to do whatever you'd like, displaying an intermediate
page with relevant code for tiling, etc. See datatypes/tabular.py's
display_data
Hi Neil,
You'll want to look at the users API controller, specifically the api_key
method. Your downstream tool could, upon receiving an empty API key from
the wrapper, generate a new key and use it (after which it'd also be
available to the user).
On Thu, Dec 5, 2013 at 9:05 PM,
around I can do in the meantime, or should I wait for your
fix?
On Mon, Dec 16, 2013 at 10:34 AM, Dannon Baker dannon.ba...@gmail.com
wrote:
Have you previously used cloudlaunch with success with this account? If
not, is this a new account created after 12-04-2013?
AWS now defaults new
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
With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have
been merged to a single 'galaxy' volume. /mnt/galaxy is now your single
persistent (by default, at least) volume, so, if you install your tool to
here and share everything should work as expected.
-Dannon
On Fri, Dec
stuff.
On Fri, Dec 20, 2013 at 2:13 PM, greg margeem...@gmail.com wrote:
Thanks. I was wrong before. I actually do see a /mnt/galaxyData.
Should I not being seeing that? Am I not on cloudman 2.0?
-Greg
On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker dannon.ba...@gmail.com
wrote
proc root run sbin selinux srv sys tmp usr
var vmlinuz
ubuntu@ip-10-182-195-79:/$ ls mnt
cm galaxyData lost+found transient_nfs
ubuntu@ip-10-182-195-79:/$ ls /mnt/galaxyData/
export files tmp upload_store
On Fri, Dec 20, 2013 at 2:20 PM, Dannon Baker dannon.ba...@gmail.com
/cloudlaunch
I chose data cluster when prompted and enter 5GB.
On Fri, Dec 20, 2013 at 2:48 PM, Dannon Baker dannon.ba...@gmail.com
wrote:
And is this a new instance you've just launched? If so, how'd you
launch
it?
On Fri, Dec 20, 2013 at 2:37 PM, greg margeem...@gmail.com
The changes you're looking at are in galaxy-central, and I'm assuming your
local codebase is tracking galaxy-dist, our release repository. You can
wait for these changes to propagate through our release process over to
galaxy-dist (I think this is scheduled to happen in early February), or, if
On Wed, Jan 15, 2014 at 3:04 PM, Cantarel, Brandi L.
brandi.canta...@baylorhealth.edu wrote:
I can see where I can upload libraries from the galaxy server, but I
can’t figure out how to load the “available” data (fastqs) — to clarify
instead of asking users to upload 5GB fastq files, which
Hey Sheldon,
My first guess is that something's going wrong with your nginx proxy/cookie
configuration. Did you happen to change this when you updated the galaxy
server at all? Have you checked the steps at
https://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy and
verified that
some time to work on this.
-John
On Thu, Jan 16, 2014 at 7:27 AM, Dannon Baker dannon.ba...@gmail.com
wrote:
On Thu, Jan 16, 2014 at 3:39 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
allow_user_impersonation does not work when using external
authentication. Are there any fixes
Hi Niel,
Galaxy does not expose filepaths to non-admin users intentionally. For
executing a workflow with that particular script, the 'file_id' in question
in that example should be an hda, which is what api/history/contents will
display for your users as the 'id' for each history item.
-Dannon
Neil
p.s. do you know where in the code it stops file_name from being
displayed (using the scripts/api/display.py script)
--
*From:* Dannon Baker [dannon.ba...@gmail.com]
*Sent:* Saturday, January 18, 2014 12:34 AM
*To:* Burdett, Neil (CCI, Herston - RBWH)
*Cc
Hi Laure,
This is intentional behavior; galaxy sanitizes all html output as a
security measure by default. You can turn this off on your instance by
changing sanitize_all_html to False in your universe_wsgi.ini.
There's a Trello card to track implementation of allowing administrators to
Galaxy was recently updated to use a newer version of webhelpers, version
1.3, in which the signatures of those methods have changed. It looks like
you're running a newer version of webhelpers (thus stylesheet_link_tag not
being found), but an older version of galaxy. I'm not sure how this would
On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
This fixed the history_dataset_association.extended_metadata_id
error - so is the most likely explanation a failed schema update?
Might a stale migration_tmp table have been to blame?
Yes, I've seen this before when
My first guess is that it's likely this is due to 'debug = True' being set
in your universe_wsgi.ini. If you set this to false and restart, the
entire request will no longer be loaded into memory.
-Dannon
___
Please keep all replies on the
The json module is included in python's standard library since python 2.6,
which is the minimum version of python Galaxy currently supports. Are you
using a python version older than that?
___
Please keep all replies on the list by using
is not picking
it up? If we can do this, then we don't need to upgrade the cluster nodes,
which is very difficult here.
Fenglou
On 20 February 2014 13:47, Dannon Baker dannon.ba...@gmail.com wrote:
The json module is included in python's standard library since python
2.6, which
If it's possible, can you check (or ask the user to check) if there are any
javascript errors if you open the browser console when experiencing this
failure?
On Thu, Mar 13, 2014 at 2:07 PM, Liisa Koski liisa.ko...@basf.com wrote:
Hello,
Our site maintains a local Galaxy installation (Nov.4th
was using the lastest Firefox release. I asked him to try FireFox
Portable and that seemed to do the trick. It was a problem with his Firefox
install.
Thanks for you help,
Liisa
From:Dannon Baker dannon.ba...@gmail.com
To:Liisa Koski liisa.ko...@basf.com
Cc:Galaxy
Hi Ricardo,
My guess is that you're running into an issue that was fixed
in 694411e94d9a. Can you verify the URL that's being pinged by the
impersonate dropdown is (in)valid? If so, pulling from stable should fix
your issues.
-Dannon
On Mon, Mar 17, 2014 at 11:24 AM, Perez, Ricardo
2014 16:31, Dannon Baker dannon.ba...@gmail.com wrote:
694411e94d9a
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface
On Tue, Apr 1, 2014 at 2:48 PM, Langhorst, Brad langho...@neb.com wrote:
However, when i add a new tool - it does not alway show up (only for one of
the workers maybe?)
I don't have good answers for the rest of your questions (I'm sure someone
else can chime in), but I do have some information
Hey Mo,
Sorry for the super delayed response here. I can't find a decision to
remove it documented anywhere, so my guess is that this tool was
unintentionally removed when we last updated the volume. It's actually
still available on disk, though, and can be re-enabled in your
tool_conf.xml by
On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote:
Hi Dannon,
Thanks for this information. Will the ENA SRA button be enabled on the
next update of Cloudman?
I'll check to make sure there wasn't a good reason to remove it (couldn't
find one in my first pass, and it's
Hey Brad, thanks for this! I've added these to the metaphlan toolshed
repository as-is, and will be adding tests shortly.
On Tue, Apr 8, 2014 at 1:24 AM, Langhorst, Brad langho...@neb.com wrote:
I'm running with these local additions to Dannon's metaphlan repo.
I think it would be better
://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets
is
how to use the command line, correct?
Thanks a lot!
Best,
Xiaofei
--
*From:* Dannon Baker [dannon.ba...@gmail.com]
*Sent:* Friday, April 11, 2014 4:42 PM
*To:* Wang, Xiaofei
*Cc
301 - 400 of 481 matches
Mail list logo
