Hi Johngui,
Can you specify which request is 404'ing -- the exact URL that's being
attempted?
And, can you provide a little more of your nginx configuration? Is galaxy
being served at the root of the domain?
-Dannon
On Wed, Nov 19, 2014 at 2:01 AM, 홍종희 wrote:
> Hi galaxy-dev members
>
>
>
Hey Ryan,
Sorry this fell through the cracks. A script to import large sets of files
to data libraries, for example, would be really easy to implement using the
Galaxy API. There are several examples in the /scripts/api folder of your
distribution (
https://bitbucket.org/galaxy/galaxy-central/sr
This is usually an old cached version of the history panel interfering, or
a javascript error that you'd see in the console.
Can you clear browser cache, close out all Galaxy windows, and try again?
If that still doesn't work, can you look in the javascript console to see
if there are any errors?
Thanks Chris, it's great to hear that Cloudman worked well for you!
There actually is a way to launch an instance providing a share-a-cluster
string in user data for a while, (a `share_string: ` entry in user
data) but there is, or was -- I need to test this again, a race condition
in the boot log
Hi Namit,
This is an oversight and that tool should be installed by default. We'll
make it so in the next Cloudman release.
That said, it's really easy to install this (and other tools) on your cloud
instances using the toolshed. Steps:
- Make yourself an admin user (see the cloudman admin int
On Mon, Oct 13, 2014 at 8:14 AM, John Chilton wrote:
> My understanding is that it was briefly optional (and maybe just
> through the API) but that was a bug. I think Dannon made that fix a
> few months ago. Sorry for the confusion.
>
This is correct, public usernames are required and there was
Legit and expected, no craziness going on there. I've never actually used
it, but my guess is it got included on this AMI from the cloudbiolinux base
we used.
On Fri, Oct 10, 2014 at 3:15 PM, Chris Dagdigian wrote:
>
> Just a paranoia check ...
>
> I manually started the cloudman galaxy AMI (am
oing anything wrong on my end.
>
> Currently launching the pure base AMI without the cloudlaunch interface
> to see if I get further ...
>
> Regards,
> Chris
>
>
> Dannon Baker wrote:
> > Just realized you said cloudlaunch in the subject there, so I'm assuming
Just realized you said cloudlaunch in the subject there, so I'm assuming
that's what you used. For both working and non-working clusters? And this
is cloudlaunch on usegalaxy.org? I can check the logs for more detailed
launch failures, if so.
On Fri, Oct 10, 2014 at 1:27 PM, Da
Hi Chris,
How are you trying to start these clusters?
And, the one you started successfully, how did you start it?
-Dannon
On Fri, Oct 10, 2014 at 1:24 PM, Chris Dagdigian wrote:
>
> Anyone else having issues using cloudman version of galaxy?
>
> No matter what set of AWS keys I use to try to
(And thanks for the catch!)
On Fri, Oct 10, 2014 at 9:48 AM, Dannon Baker
wrote:
> D'oh. It's correct in the block right above that, but incorrect there.
> I'll fix it now.
>
> On Fri, Oct 10, 2014 at 9:44 AM, Nicola Soranzo wrote:
>
>> Hi Dannon,
>>
roject.org/Admin/Config/nginxProxy is
> still wrong?
>
> Ciao,
> Nicola
>
> Il giorno ven, 10/10/2014 alle 08.50 -0400, Dannon Baker ha scritto:
> > Just to follow up on this thread -- we resolved this over IRC. It was a
> > proxy configuration issue with nginx's
Just to follow up on this thread -- we resolved this over IRC. It was a
proxy configuration issue with nginx's upload_config settings.
Correct settings are now on the wiki, but the previous rule for: location
_upload_done : "set $dst /tool_runner/index;" is was causing a redirect and
preventing
y instructions around, how to implement a rabbitmq for my
> Galaxy?
>
> Thanks for looking into this.
> Ulf
>
> On 08/10/14 11:26, Dannon Baker wrote:
> > Hi again Ulf,
> >
> > Thanks for the info. A few questions to help me track this down:
> >
> > Doe
ss after both
> dependent classes have been defined.
>
> ---
>
> After that it starts throwing the exception in monitor_step that I
> previously posted. Has anyone seen a potentially related issue? Would an
> update to the latest galaxy code help? I see there are newer ver
One per second? Can you tell me more about your configuration? This is
an odd bug with multiple mapper initialization that I haven't been able to
reproduce yet, so any information will help. Database configuration,
number of processes, etc.
On Oct 7, 2014 11:46 AM, "Ulf Schaefer" wrote:
> Dea
Hi Viren,
There's a script shipped with galaxy that you can use
'./scripts/set_user_disk_usage.py' to force recalculation of a user's disk
usage.
-Dannon
On Tue, Sep 30, 2014 at 7:44 PM, Patel, Viren wrote:
> Hello. I have a Galaxy user whose disk usage remains at 91% even after
> deleting and
rsity of NY at Buffalo
>
> Center for Computational Research
>
> 701 Ellicott St
>
> Buffalo, NY 14203
>
> Phone: (716) 881-8934
>
> Fax: (716) 849-6656
>
> Web: http://ccr.buffalo.edu
>
> **
>
>
>
>
>
>
>
&
as output of workflow for each of this 2 step.
> The dataset of my first step is hidden and deleted : good!
> But the dataset of my second step is hidden but not deleted ! I don't
> understand why
>
> Thanks
> Julie
>
> 2014-09-23 15:49 GMT+02:00 Dannon Baker :
>
>&
an output of a job not used in an other job.
>
> Is an hidden dataset not deletable ?
> I've changed the order of postJobActions in the file, but no effect.
> And If I remove the "HideDatasetAction", the dataset is not removed
> because it become marked with highligthed
Hi Julie!
The action resolves at the completion time of the job it is attached to,
deleting datasets of any other already-completed jobs in that workflow
which are not marked as an output step (with a highlighted snowflake).
This will *not* delete datasets of any job marked as an output.
Perhaps
Hi Pieter,
I updated the jQuery library that ships with galaxy in
revision 14425:068fa60b8c2b on August 19, which should hopefully have
resolved these issues. Are you still seeing problems on a galaxy server
updated past that revision?
-Dannon
On Fri, Sep 19, 2014 at 4:45 AM, Lukasse, Pieter
w
Hi Tim,
Thanks for this. If you still have it handy, what was the exact attribute
error?
-Dannon
On Thu, Sep 18, 2014 at 10:28 AM, Tim Booth wrote:
> Dear Devs,
>
> I recently ran into a problem where attempting to run a workflow
> resulted in an uninformative error and a traceback in the log
Hi George,
I'd think something is a bit wonky if it needs to be that big. Mind
sharing what's in there and why it needs to be so large?
-Dannon
On Wed, Sep 17, 2014 at 4:59 PM, George Weingart
wrote:
> Hello,
>
> I have an application that is working perfectly in our local Galaxy (Not
> using
Hey Ashish,
We have an open issue to sort out exactly why/how this happens, but a quick
fix for many users is just to remove your eggs/ folder and all eggs and
re-run `python scripts/fetch_eggs.py`. Give that a shot, but do let me
know if it doesn't' work.
On Wed, Sep 10, 2014 at 4:54 PM, ashis
nesota Supercomputing Institute
> 599 Walter Library
> 612 624 1447
> e...@msi.umn.edu
> boll0...@umn.edu
>
>
> On Thu, Aug 21, 2014 at 4:20 PM, Dannon Baker
> wrote:
> > There is no reason workflow invocation *has* to be synchronous, but
> that's
> > how
There is no reason workflow invocation *has* to be synchronous, but that's
how galaxy works right now as, mostly, a historical artifact. Workflow
scheduling happens inside the web request, and other than bioblend issuing
the request in another thread there won't be an implementation w/ no_wait.
T
Hey David,
I'm not sure why you'd be having this issue, but I'd contact the RNA-Rocket
server staff (pathporth...@vbi.vt.edu) for more assistance; this is not a
Galaxy server that the Galaxy Team manages.
-Dannon
On Thu, Aug 21, 2014 at 9:51 AM, David Salcines
wrote:
> Hi, I was trying to upl
It's currently not possible to build loops into galaxy workflows. Major
workflow engine enhancements are being worked on, but for an immediate
solution you could drive something like this using the API if you wanted to.
-Dannon
On Thu, Aug 14, 2014 at 8:54 AM, Görkem Erdoğan
wrote:
> Hello Al
Thanks for the update, glad everything is working as expected!
On Wed, Aug 13, 2014 at 12:27 PM, Tony Kusalik wrote:
> My apologies to everyone. This turns out to be a false alarm.
> The problem was caused by a strange, intermittent issue with the
> DNS servers on our campus (I'll spare you th
Hey Tony,
Thanks for the error report. I'll look into this, but you can try two
things really quickly to see if you can get galaxy started:
1) python scripts/fetch_eggs.py may fix up your egg situation
2) just delete the eggs folder of your galaxy distribution
(/eggs) and start galaxy again. It
dcb67f" at character 2721
> > postgresql-Wed.log:< 2014-08-06 15:04:26.964 EDT >ERROR: invalid input
> > syntax for integer: "a328cf0b6432c591" at character 2721
> > postgresql-Wed.log:< 2014-08-06 15:20:06.512 EDT >ERROR: invalid input
> > syntax f
P/1.0" 200 - "
> http://galaxy.neb.com/root/index"; "Mozilla/5.0 (Macintosh; Intel Mac OS X
> 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125
> Safari/537.36"
> 172.17.131.223 - - [01/Aug/2014:17:15:08 -0400] "GET
> /api/histories/11ff4619
Hi Don,
Haven't seen this before myself, but I did a little digging here:
http://docs.sqlalchemy.org/en/rel_0_8/faq.html#mysql-server-has-gone-away
So, to differentiate between those two issues, does this happen very
frequently or only after a long idle?
-Dannon
On Wed, Aug 6, 2014 at 3:15 PM,
> ./tool_conf.xml, but only after the installation process finishes.
>
>
>
> On Wed, Aug 6, 2014 at 10:53 AM, Dannon Baker
> wrote:
>
>> Ahh, I think I see the issue. So, many galaxy tools are being migrated
>> out of the distribution and to the toolshed -- you can f
tools even I could see
> it...could you please let me know how I could configure this?
>
> Thanks,
> Rui
>
>
> On Wed, Aug 6, 2014 at 10:23 AM, Dannon Baker
> wrote:
>
>> Hi Rui,
>>
>> We'll definitely take a look. Please allow for a reasonable time per
Hi Rui,
We'll definitely take a look. Please allow for a reasonable time period to
pass before sending duplicate emails to the list asking for assistance.
That said, does deleting your integrated_tool_panel.xml (this file is
automatically regenerated by Galaxy, safe to remove it and restart) bri
Definitely looks like an encoded id is being used in the query when it
should be an unencoded id. I can try to dig through the query and make
guesses as to what's calling it, but do you have any hints at all what's
happening in galaxy at the time of this request?
-Dannon
On Tue, Aug 5, 2014 at
There's definitely a request that will occasionally block at startup --
I've hit this before too, Martin. Looking into it now.
On Tue, Aug 5, 2014 at 2:59 PM, Martin Čech wrote:
> I just freshly cloned galaxy-central, switched to next-stable and did
> initial startup - no problems detected and
The method John suggests is definitely a better way to get the user's API
key.
That said, the 'get' change is due to sqlalchemy version changes that
happened quite a while back. You can no longer 'get' directly from the
model, you must use a query object. So, for example, this line:
model.U
-E
> -Evan Bollig
> Research Associate | Application Developer | User Support Consultant
> Minnesota Supercomputing Institute
> 599 Walter Library
> 612 624 1447
> e...@msi.umn.edu
> boll0...@umn.edu
>
>
> On Mon, Aug 4, 2014 at 2:32 PM, Dannon Baker
> wrote:
> >
Hi Evan,
What you're looking for should be covered by the new Job Metrics plugins.
If you'd like to know more, see:
https://wiki.galaxyproject.org/Admin/Config/JobMetrics
-Dannon
On Mon, Aug 4, 2014 at 3:24 PM, Evan Bollig wrote:
> Jobs executed in the workflow appear to have a creation time
Hi Dori,
If you haven’t updated galaxy or manipulated the eggs at all, then it might be
an updated system python module interfering with galaxy’s resolution of the
pyyaml we ship. Can you try running galaxy from an clean virtualenv?
(https://wiki.galaxyproject.org/Admin/Config/Performance/Prod
Hi Iyad,
`find -name '*.pyc' -delete`
Should clean up compiled python files allowing you to run again.
-Dannon
On Tue, Jul 22, 2014 at 11:16 AM, Kandalaft, Iyad
wrote:
> Hello everyone
>
>
>
> I tried a galaxy update on my development instance of galaxy. It failed
> due to a schema change
Hi Mark,
You may want to look into using Data Libraries for large imports like this
-- it'll allow you to import the files into Galaxy without making an extra
copy. See
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
for more information -- specifically the 'allow_library
Hi Pablo,
1) I have read in the wiki that it's only available in region US East
> (Virginia). Will it be available in Ireland region?
>
This is currently true, though we're hoping to mirror to other regions soon.
> 2) I see I need to attach EBS volumes to my head node to host the
> software and
How large are the files you're attempting to upload?
Another method for uploading with more reliability than web browsers would
be to use FTP. See the documentation here for more details:
https://wiki.galaxyproject.org/FTPUpload
-Dannon
On Tue, Jul 8, 2014 at 9:45 AM, Matthew Birnie wrote:
>
No, since the integer X relates the file on disk to the Dataset object in
the database. Technically, you could probably pull it off if you wanted to
perform a bunch of database surgery, but I'd really not recommend it.
-Dannon
On Fri, Jul 4, 2014 at 3:43 AM, Pat-74100
wrote:
> Dear Galaxy dev
Jan is correct, this is what Galaxy does.
-Dannon
On Wed, Jun 25, 2014 at 6:29 AM, Jan Kanis wrote:
> Probably the same way by which it keeps track of you when you are logged
> in: setting a cookie in the browser. I didn't verify this, but that is how
> basically all web services do it. If you
ght now an attacker would be stealing your cookie
> information")http://i.imgur.com/2ZTC4gh.jpg "/>
>
>
>
>
>
> Neil
>
> *From:* Dannon Baker [mailto:dannon.ba...@gmail.com]
> *Sent:* Wednesday, 18 June 2014 10:55 PM
> *To:* Burdett, Neil (CCI, Herston - RBWH)
>
Hi Neil,
Galaxy definitely takes this sort of thing very seriously. I'll take a
look at the possible XSS locations identified in the report and verify
whether or not they're actually vulnerable.
For Denial of Service attacks, I'd suggest that this should be handled by
the upstream proxy.
You sh
This is a new one for me. What configuration are you using for both your
'database_connection', and the 'amqp_internal_connection' in your
universe_wsgi.ini?
On Fri, Jun 13, 2014 at 12:29 AM, xlwang wrote:
> Hello,
> when i run my galaxy instance type:
> $ sh run.sh
> I get some error like
Hey Hans (and anyone else using MySQL),
Just to clarify -- MySQL doesn't have this (particular) error by default
and as long as your server default table type has not and does not change
you should be fine. I've just successfully tested MySQL using MyISAM all
the way to the current tip revision a
Hey Iyad,
I just want to second (and add slightly) to what John said here. I had
also failed to reproduce this locally, but that makes perfect sense now --
I'm glad you figured it out, and thanks for looking into this so closely
and reporting back.
Like John said, I wouldn't modify the migration
Hey Stephen,
Can you look in the server logs to see if there are any errors being
reported? Or if there are any javascript errors in the browser window?
You may also want to try clearing your browser cache.
-Dannon
On Tue, Jun 10, 2014 at 1:54 AM, Stephen E wrote:
> I installed a local inst
69, in resolve
> raise VersionConflict(dist,req) # XXX put more info here
> pkg_resources.VersionConflict: (bioblend 0.4.2
> (/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
> Requirement.parse('simplejson'))
>
> Simplejson is installed i
> to this mailing list.
>
> -E
>
>
> On Wednesday, June 4, 2014, Dannon Baker wrote:
>
>> Hey Nikos,
>>
>> I think you're seeing the same issue from this trello card here:
>> https://trello.com/c/HWuxsftB/1596-fetching-zip-safe-eggs-that-depend-on-other-
Hey Nikos,
I think you're seeing the same issue from this trello card here:
https://trello.com/c/HWuxsftB/1596-fetching-zip-safe-eggs-that-depend-on-other-eggs-will-fail
Can you run `python scripts/fetch_eggs.py` from your galaxy directory?
That should re-fetch galaxy's eggs and you should be up
I'm having trouble reproducing this. The base grid object that's used by
the SpecifiedDateListGrid does have that info_text field -- it's almost as
if you're somehow using an outdated grid module, while the rendering
template is current.
It's a bit brute force, but can you try (from the base of yo
Hey Iyad,
This is an area under active development. You can track the progress of it
on this card here: https://trello.com/c/nwYQNFPK/56-data-library-evolution
The new data libraries are *much* faster, and if you'd like to enable them
for your local site. You should be able to see this in curr
to figure out how to get my data in...
> ________
> From: Dannon Baker [dannon.ba...@gmail.com]
> Sent: Tuesday, May 27, 2014 11:43 AM
> To: Paniagua, Eric
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database
> on a remote
On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric wrote:
> Thanks for pointing that out! I missed it. I am now connecting to the
> remote database. I ran "sh manage_db.sh upgrade" and it upgraded from
> schema 114 to 118 without error messages. I then ran "sh
> ./scripts/migrate_tools/0010_too
Cross-post from biostar, answered there:
https://biostar.usegalaxy.org/p/7747/#7760
On Mon, May 26, 2014 at 6:47 AM, Julien Daligault <
daliga...@ijm.univ-paris-diderot.fr> wrote:
> Hi,
>
> I manage a galaxy instance on a local server and I want that users use
> only the "filesystem paths" to cr
Hey Eric,
It looks like you have connection info for both tcp/ip connections and unix
sockets in the connection strings. If you're logging in using "psql -h
wigserv5.cshl.edu ", then you only want the tcp/ip connection info.
Drop the ?host=tmp off the third option you listed and I think you'll b
Hey Peter,
By default, galaxy attempts to ship 50kb chunks of tabular data. It's a
good idea to probably support a minimum number of 'lines' to ship as well,
for text-based data -- I'll add a Trello card for this and will plan to
work on it soon.
That, and there should be an indicator along the
On Fri, May 23, 2014 at 9:07 AM, Greg Von Kuster wrote:
> I'm not quite sure whether this baseline implementation will handle
> comunication between Galaxy web front-ends like you have (and like we have
> for our public Galaxy instances).
>
Yep, it sure does. There's still a little bit of work
Yep, your guess looks correct. We enforced creation of a public username
at registration a long while back, but it looks like the API doesn't do the
same enforcement (and neither does the web interface, anymore -- d'oh).
I'll get a bugfix out shortly.
On Thu, May 22, 2014 at 11:12 AM, Evan Boll
Hi Evan,
It looks like that message might actually list the two versions backwards.
I'll check into it and, if that's the case, get a fix out shortly.
In any event, you should be able to edit and re-save the workflow as
indicated to keep moving forward.
-Dannon
On Tue, May 20, 2014 at 3:02 PM
t;
> Cheers,
>
> -E
> -Evan Bollig
> Research Associate | Application Developer | User Support Consultant
> Minnesota Supercomputing Institute
> 599 Walter Library
> 612 624 1447
> e...@msi.umn.edu
> boll0...@umn.edu
>
>
> On Fri, May 16, 2
On Fri, May 16, 2014 at 3:33 PM, Evan Bollig wrote:
> InvalidVersionError: 103 is not 105
>
This would indicate to me that migration script 104 failed.
My question is: why can't the manage_db.sh upgrade step be included
> automatically when the initial DB build fails?
>
It is, in a sense, henc
t 11:15 AM, Peter Cock wrote:
> On Mon, May 5, 2014 at 3:47 PM, Dannon Baker
> wrote:
> > On Mon, May 5, 2014 at 10:32 AM, Peter Cock
> > wrote:
> >>
> >> However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg
> >> the old error persists. Is
On Mon, May 5, 2014 at 10:32 AM, Peter Cock wrote:
> However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg
> the old error persists. Is there a case-sensitivity issue here (PyYAML
> versus pyyaml)?
>
Yep, I've adjusted that now and my guess is it'll work next time.
Let me know if
Can you add a `python scripts/fetch_eggs.py` to your travis config just
after the stop-daemon? That should parse eggs.ini and fetch all of the
eggs.
On Mon, May 5, 2014 at 9:51 AM, Peter Cock wrote:
> On Mon, May 5, 2014 at 2:30 PM, Dannon Baker
> wrote:
> > Hey Peter,
> >
&
Are you using usegalaxy.org?
This generally indicates a temporary error with one of our cluster node (if
using usegalaxy.org), or a misconfiguration of the job management system if
you're seeing this on a local cluster. If you're using usegalaxy.org I'd
recommend simply retrying the upload.
-Dan
Hey Weiyan,
You can't (currently) specify disk destinations per user, but you can
certainly use multiple disks in a pool. For one example, see the sample
object store configuration here (and also in your galaxy distribution):
https://bitbucket.org/galaxy/galaxy-central/src/92519a9bfa32a42ce47a63f
Hey Peter,
Just looking at the travis job, it looks like there's not a fetch_eggs step
at the start, but rather that it's fetching as they're require()'d. Is
that correct? In any event, I'm changing the order of those requires
in 13302:92519a9bfa32, which may resolve your issue. They work fine
Hi Jess,
I've recalculated your disk usage, you should be good to go now.
-Dannon
On Mon, Apr 28, 2014 at 11:51 AM, Jess Gaunt wrote:
> Dear Ido,
> Thank you for your response, but I don't have a usage question. I've read
> through all of the information on managing datasets and it seems to be
say, 15 seconds instead of 60.
>
> Jim
>
>
> On Mon, Apr 28, 2014 at 2:05 PM, Dannon Baker wrote:
>
>> The time after which it culls instances? It is not, but because of the
>> way Amazon bills for instances, you never want to kill an instance until
>> the e
at 3:01 PM, Jim McCusker wrote:
> Thanks, is the idle time configurable?
>
>
> On Fri, Apr 25, 2014 at 2:43 PM, Dannon Baker wrote:
>
>> You can review the exact code here( see 'slow_job_turnover') :
>> https://bitbucket.org/galaxy/cloudman/src/7b8f04895a
You can review the exact code here( see 'slow_job_turnover') :
https://bitbucket.org/galaxy/cloudman/src/7b8f04895ad309e0168cb3de66446ae20f3d8b3e/cm/services/autoscale.py?at=default
But, basically, load on any particular node isn't very useful for
autoscaling in this context because most jobs cann
ttp://127.0.0.1:8080/api/workflows f2db41e1fa331b3e a799d38679e985db
> '10=hda=52ea4fd71e9f7c3f' 'param=export_sbw=prefix=test'
>
> Could you help me on that ? How do I give a value to a parameter if it
> does not appear in the WF description ??
>
> Thanks in
tafor how to specify
that in your UserData.
-Dannon
On Fri, Apr 25, 2014 at 11:13 AM, Dannon Baker wrote:
> Hi Jim,
>
> /mnt/galaxy is shared via NFS with all cluster workers -- this (or a
> subdirectory) should work for you.
>
> -Dannon
>
>
> On Fri, Apr 25, 2014 at
Hi Jim,
/mnt/galaxy is shared via NFS with all cluster workers -- this (or a
subdirectory) should work for you.
-Dannon
On Fri, Apr 25, 2014 at 10:56 AM, Jim McCusker
wrote:
> Hi all,
>
> I need to add a .boto file to the user that galaxy jobs get exec'ed as on
> cloudman nodes. I thought it w
efault options for my jobs and the same workflow
> has been working fine for me in the past on the same datasets.
>
> Thanks for any help you can give me!
>
> Alessia
>
>
>
> On Apr 24, 2014, at 10:24 PM, Dannon Baker wrote:
>
> Hey Alessia,
>
> I'd lo
Hey Alessia,
I'd love to help, but I need a little more context here. Where are you
seeing this error, what exactly are you doing when it appears, and can you
tell me a little bit more about the Galaxy configuration you're working
with?
-Dannon
On Thu, Apr 24, 2014 at 8:37 PM, Jennifer Jackson
Hi Olivia!
It's probably talking about the "workflowstep" object with identifier 8.
If you request the description of this workflow via the API (
http://yourgalaxyinstance.org/api/workflows/"),
you'll be given the exact step identifiers to use. In other words, unless
this is the first workflow e
Hi Milad,
That's just a warning, it should not cause any issues (I've just confirmed
this locally on a sqlite instance). So you're sure you have histories with
deleted datasets older than 0 days? The commands you have run will not
remove datasets that haven't been deleted first by a user (usuall
my mail and in your script
> : should be migration_tmp instead of migrate_tmp;)
>
>
>
> Best regards,
>
>
>
> Pieter.
>
>
>
> *From:* Dannon Baker [mailto:dannon.ba...@gmail.com]
> *Sent:* dinsdag 22 april 2014 14:59
> *To:* Lukasse, Pieter
> *Cc:* Peter
> database
>
>
>
> Thanks and regards,
>
>
>
> Pieter.
>
>
>
> *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto:
> galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Dannon Baker
> *Sent:* dinsdag 18 februari 2014 14:40
> *To:* Peter Cock
> *Cc:* Galaxy Dev
&
Giga level
please let us know.
We hope to see you in June, and can't wait to see what we can accomplish!
-Dannon Baker on behalf of the GCC2014 Hackathon Organizing Committee
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55 PM, Dannon Baker wrote:
> Hey, sure. The option you're looking for is "allow_user_dataset_purge",
> around line 650 or so.
>
> Good luck!
>
> -Dannon
>
>
> On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei wrote:
>
>> Hi Dannon,
>>
>>
What I see from here
> https://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]
Hi Xiaofei,
The (x) simply flags a dataset for deletion, it does not remove it from
disk. This happens when the instance maintainers run cleanup scripts. If
your instance is so configured, you can use the "Purge Deleted Datasets"
option to immediately remove datasets from disk.
-Dannon
On Fri
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 wrote:
> I'm running with these local additions to Dannon's metaphlan repo.
>
> I think it would be better to add these to
On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian wrote:
> 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 available on m
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 add
On Tue, Apr 1, 2014 at 2:48 PM, Langhorst, Brad 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 about this. Yo
find /api/user on the server
> root.
>
> Thanks,
>
> Eric
>
>
> On 17 March 2014 16:31, Dannon Baker wrote:
>
>> 694411e94d9a
>
>
>
>
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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 wrote:
>
Liisa Koski wrote:
> Our use 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
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