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 wrote:
> Hello,
> Our site maintains a local Galaxy installation (Nov.4th distributuion).
>
dule in galaxy-dist/eggs, why Galaxy 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 wrote:
>
>> The json module is included in
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 "rep
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 l
On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock wrote:
> 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 I've killed (or otherw
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
Ketan,
Have you taken a look at galaxy's built-in parallelism framework? For a
great current example of a tool using this, look at Peter's NCBI BLAST+
wrappers. https://github.com/peterjc/galaxy_blast
-Dannon
On Thu, Feb 6, 2014 at 10:32 AM, Ketan Maheshwari <
ketancmaheshw...@gmail.com> wrot
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
indivi
7;s the last entry in
> /history/contents. So given only a database_'id'.dat filename how can I get
> the history id dynamically with no user interaction and not being an admin
> user?
>
> Thanks for any help
> Neil
>
> p.s. do you know where in the code it stops fil
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
> some time to work on this.
>
> -John
>
> On Thu, Jan 16, 2014 at 7:27 AM, Dannon Baker
> wrote:
> > On Thu, Jan 16, 2014 at 3:39 AM, Hans-Rudolf Hotz wrote:
> >>
> >> "allow_user_impersonation" does not work when using external
> >>
On Thu, Jan 16, 2014 at 3:39 AM, Hans-Rudolf Hotz wrote:
> "allow_user_impersonation" does not work when using external
> authentication. Are there any fixes for this in progress?
>
> If not shall I create a Trello card?
>
If there's no Trello card for it, I doubt it's currently being worked on.
Would direct-sharing histories work as a significantly lighter weight
solution? Each student could just create a history named
"DannonBaker_SharedResults" or the like, share it directly with their
instructor, and put via dataset copy and/or perform any work to be shared
in that?
-Dannon
On Wed,
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 (
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, whi
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
thi
ere and filled out the form:
> > https://usegalaxy.org/cloudlaunch
> >
> > I chose "data cluster" when prompted and enter 5GB.
> >
> >
> > On Fri, Dec 20, 2013 at 2:48 PM, Dannon Baker
> wrote:
> >> And is this a new instance you've
t; media mnt opt 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
atest stuff.
On Fri, Dec 20, 2013 at 2:13 PM, greg 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
> wrote:
> >
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 20,
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 too
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
> wrote:
> > Have you previously used cloudlaunch with success with this account? If
> > not, is this a new account created after 12-04-2013?
> >
> &
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 accounts to using EC2-VPC (and it doesn't look like
there's any way to switch back to EC2 classic) and this unfortunately
conflicts with cloudman's sec
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, wrote:
> Hi
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 meth
On Tue, Dec 3, 2013 at 5:49 AM, Bjoern Gruening
wrote:
> 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 discs are full
On Wed, Nov 20, 2013 at 9:07 AM, Manisha Sapre 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 keep all r
effective way 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
>
> Fro
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
instance
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?
>
> Warm
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 offli
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 wrote:
> On Wed, Nov 13, 2013 at 10:34 AM, Peter Cock
> wrote:
> > On
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
addin
dd
> Should this be a problem with root access ? Thanks
>
> From: Dannon Baker
> Date: Tuesday, October 29, 2013 10:25 AM
>
> To: System Administrator
> Cc: "galaxy-dev@lists.bx.psu.edu" , David
> Roe
> Subject: Re: [galaxy-dev] cloning Galaxy cluster on cloud
isha Sapre wrote:
> Yes , all users have been allotted a private key , this error is after
> ssh-add ( private key),
>
> From: Dannon Baker
> Date: Tuesday, October 29, 2013 10:15 AM
> To: System Administrator
> Cc: "galaxy-dev@lists.bx.psu.edu" , David
> Roe
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 wrote:
> Good Morning Dannon
>
> we have paid ama
And I can answer the first part; this is a known issue we're trying to
nail down and get a fix out for this week, along with a base volume update
to address other issues. Trello card: https://trello.com/c/8XSIeoG0
On Tue, Oct 15, 2013 at 10:23 AM, Peter Cock wrote:
> On Tue, Oct 15, 2013 at 10
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 p
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 wrote:
>
>> Nothing formal. The .ga extension is simply the
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
If you look at the attribute details for one of your fastq files, what does
Galaxy say the filetype is? You most likely need to flip it from 'fastq'
to 'fastqsanger' so Galaxy will know how to handle the file, it doesn't
automatically detect this.
-Dannon
On Mon, Oct 7, 2013 at 10:38 AM, UMD Bi
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 t
Have you tried to use data libraries for this? There's an import mechanism
there that'll allow you to simply link to the file on disk without
copy/upload. I believe the "example_watch_folder.py" sample script (in the
distribution) does just this via the API, if you want an example.
On Mon, Sep
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 wrote:
> Howdy,
>
> On our local galaxy cluster, I have go
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 wrote:
> Hi All,
>
> I'm trying to do some cleanup in my test environment (galaxy
;
> On Thu, Sep 5, 2013 at 5:31 PM, Dannon Baker wrote:
>
>> 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
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 wrote:
> Hi All, Is there any update on iRods integration in galaxy ? One major
> concern pr
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 wrote:
> On Aug 29, 2013, at 11:50 AM, Nate Coraor wrote:
>
> > On Aug 26, 2013, at 5:03 AM, Christophe Antoniewski wrote:
> >
> >> Hi everybody,
>
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 oth
s 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 wrote:
> On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock wrote:
&
On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock wrote:
> 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 which therefore have
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 wrote:
> Hey Peter,
>
> I
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 t
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 wrote:
> Hi all,
>
> I have found two
gt; Anto Rajkumar, MD, DNB, MRCPsych,
> PhD fellow, Department of Biomedicine,
> Aarhus university,
> 8000 C, Aarhus, Denmark.
> E-mail: a...@hum-gen.au.dk
> --
> *From:* Dannon Baker [dannon.ba...@gmail.com]
> *Sent:* 16 August 2013 15:53
>
&g
e admin values provided ([]) or Galaxy service not found
> Current Galaxy admin remains as cl...@galaxyproject.org.
> Where do I go wrong?
> How do I create the new admin user?
>
> Best wishes,
> Anto
>
>--
> *From:* Dannon Baker [danno
Hi Anto,
Yes, you should be able to create an admin user for your galaxy
installation via the cloudman admin panel
(http:///cloud/admin)
in as an admin. Once you're an admin user, you'll see the toolshed
installation stuff in the galaxy admin panel.
-Dannon
On Fri, Aug 16, 2013 at 6:03 AM, Ant
There aren't any database-specific tests, but if you could get more details
from your sysadmin regarding the issues they're seeing, I'd be very
interested in seeing it.
You could run the usual functional tests to verify galaxy itself is
functional: http://wiki.galaxyproject.org/Admin/Running%20Tes
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 actuall
On Thu, Aug 8, 2013 at 4:57 PM, Ravpreet Setia wrote:
> 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 further reply that the worka
oly, 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
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-da58aab3&bucket_default=gxy-workshop
On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly <
ulyanov_anat...@allergan.com> wrote:
> H
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, B
@oicr.on.ca]
> *Sent:* 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 p
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 wrote:
> Good day!
>
> While I was uploading the file (through FileZilla), I encountered this
> message box
te:
> HI - did you find anything with the share string? Thanks, Deniz
>
>
> On Fri, Jul 26, 2013 at 3:32 PM, Dannon Baker wrote:
>
>> 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
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-da58aab3&bucket_default=gxy-workshop
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 wrote:
>
>
>
>
> Hi Dannon,
>
> Thank you very much for replying. The problem is that we cannot display
> any tabular files in th
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 wrote:
>
>
> Hi everybody,
>
>
> In my lab, after upgrading our Galaxy instance to the latest version, we
> have a problem with displayi
June. The problem arose
> 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 wrote:
>
>> On Thu, Jul 25, 2013 at 4:47 PM, Deniz Erezyilmaz wrote:
>>
>> The workaround d
On Thu, Jul 25, 2013 at 4:47 PM, Deniz Erezyilmaz wrote:
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-da58aab3&bucket_default=gxy-workshop)?
This should launch the pre
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 wrote:
> Hi everybody
>
> Since yesterday all processes I have r
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. T
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
wrote:
> I tried launching an instance specifying "ami-da58aab3" as the AMI but I
> am unable to SSH or access Cloudman using the instance's URL.
>
> __
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
wrote:
>
>- This is what has been reported by the cluster status log:
>-
>- 20:01:14 -
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 pre-conferen
On Mon, Jul 1, 2013 at 8:34 PM, Brad Chapman 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 privileges, here'
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
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, sin
Marley,
For questions pertaining to the main instance, please email galaxy-user or
galaxy-bugs. I'll follow up in a second email with details about your account.
-Dannon
On Jun 22, 2013, at 11:03 AM, Marley Yeong wrote:
> Dear sir or madam,
>
> It seems my profile has been deleted, before
h a fresh installation of version
> 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
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 extens
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 wrote:
> This is actually a bug in the current tip of galaxy-central that we should
> have resolved s
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 wrote:
> Hi,
>
> Just setup G
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
th
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 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
dispatchin
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 wrote:
> Hello dev-team,
>
> Usually when I wa
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) f
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 wrote:
> The SQLAlchemy "postgres" dialect was renamed to "postgresql". Changing:
>
>
On Jun 6, 2013, 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 branc
3 -0400
> summary: Update tag for stable_2013.06.03
>
> script/manage_db.py still the same as above.
>
>
> [image: Inactive hide details for Björn Grüning ---06/05/2013 04:30:09
> PM---Hi Linda, > Hi Dannon,]Björn Grüning ---06/05/2013 04:30:09 PM---Hi
> Linda, > Hi
-python-2-7-2
On Thu, Jun 6, 2013 at 4:19 PM, Andrew Krohn 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 wrote:
>
>> Ho
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 wrote:
> I looked through others' problems, but this seems unique. I just did a
> clean ins
ote:
> 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
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 wrote:
> Thanks for confirmation Björn.
>
> Pull request was submitted:
> h
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 wrote:
> Hi. I am new to the Gala
Upload via browser is likely to fail when file size is > 2G, but since the
filesystem is local, you have a few extra options. You'll need to be
logged in as an admin to use the functionality, but if you enable
allow_library_path_paste (in universe_wsgi.ini), you can create datasets in
a data libra
On Fri, May 31, 2013 at 9:51 AM, John Chilton 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 keep all replies on t
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, Joac
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