On 06/12/2014 12:06 AM, John Chilton wrote:
If anyone out there has tired using Galaxy with strictly MyISAM tables
and found it untenable - by all means please chime in.
Well, due to several reasons we are (still) using MySQL (version:
5.1.69) with only MyISAM tables. We have been runnin
Thank you, Iayd. Indeed, setting ulimit -s to unlimited helped to advance
this further.
I can see now that a job gets generated and submitted. However Galaxy
crashes immediately after that.
Job <108038> is submitted to queue .
*** glibc detected *** python: free(): invalid pointer: 0x7fff79f10b
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
https://trello.com/c/AGKePuHZ/1630-expose-use-remote-user-via-configuration-api
I don't know if this is the correct card (it's been a long day and I may
be misreading it) but the API is completely broken under REMOTE_USER
authentication.
running ./sc
On Wed, Jun 11, 2014 at 3:26 PM, Kandalaft, Iyad
wrote:
> Dannon & John,
>
>
>
> Thank you for your feedback. I agree that documentation is a good start.
>
>
>
> I’m still in the process of figuring out what actually happens to the
> database schema. It may be completely fine with no referential
Dannon & John,
Thank you for your feedback. I agree that documentation is a good start.
I’m still in the process of figuring out what actually happens to the database
schema. It may be completely fine with no referential integrity constraints,
which I’m okay with to some degree (we’re still i
Hi Kozin,
Are you using a python environment specifically for galaxy? If not, then jobs
running on the compute will be using the wrong python environment. I setup
galaxy (universe_wsgi.ini option) to source the python environment for galaxy
before every job.
Galaxy is coded to work only if i
I am now able to export capsules from the main/test toolsheds -- thanks
Dave! When attempting to import these capsules into my local toolshed
(latest_2014.06.02
for changeset fb68af9a775a) I receive the following error:
URL: https://galaxy.lygos.com:99/repository/import_capsule
File
'/home/galaxy/
Will,
Thank you for reporting this issue, it has been fixed as of
13827:5b67e047172f and 13826:0af48b3c8f33, which are now running on the
test and main tool sheds. The change to the stable branch will be
pushed to the galaxy-dist repository within a few days.
--Dave B.
On Wed 11 Jun 2014
I am running local toolshed with a recent version (latest_2014.06.02 for
changeset fb68af9a775a). When viewing one of my tools, I can click on the
'Repository Actions' button and see the option 'Export this revision.' When
I am using the public main or test toolsheds, I don't see the 'Export this
r
Hi Sarah,
Data libraries are in an active enhancement phase. There are many
changes recent, in progress, and planned that you can review in Trello.
This is one of them, and the specific card is here:
https://trello.com/c/0RnzM6lP
For now, uploading with the name you wish to use in the UI is
Hello Julien,
I don't know if you have had help already or not, but contacting the
owners of this instance is the probably the quickest path to an answer
(and possibly shared code). At this instance, under "Help -> Support",
they have modified the link to point to the email address for their
Hello,
This question and this Biostar post are the same question, correct?
https://biostar.usegalaxy.org/p/7979/
Glad this is resolved. Next time, would be best to post to just one place.
Thanks!
Jen
Galaxy team
On 6/10/14 3:55 AM, Israel Bravo wrote:
When trying SAM/BAM to Counts I get the
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
Spent a couple hours yesterday trying to track down this - I was not
getting anywhere though and I see why now.
Well this definitely an unfortunate situation - but I think
documentation improvements are the right fix not enforcing the engine
type in sqlalchemy migrations. For one, I don't think we
Derp... that is a result of the change I just made. I'll see if I can add a
line that checks to see if the uploaded file is a folder and sets it to 0755 if
that is the case. Seems like a security risk to just do a blanket 0755 and let
people upload executable files.
If (path is a file)
This is a follow up for those that are interested with regards to my failed
schema upgrade.
I believe I have determined why all the tables are set to use the MyISAM
engine. When I initialized galaxy on our enterprise servers, they were running
a dated version of CentOS. Hence, the OS defaults
Hi John,
Here is what I've tracked down this morning. On the off chance this seems
wildly off the mark I don't know much about python or galaxy. I am drinking
fancy coffee though ;)
I did confirm all the folders are world executable. The upload is running as a
local job, not a cluster job.
So the permissions on these files seem fine right. That is odd.
Next things I would check are that each directory leading up to
/panfs/storage.local/scratch/galaxy-data/ is world executable and that
the whole thing (/panfs/storage.local/scratch/galaxy-data/) is mounted
and with the same permission
Hi Vipin,
Can you elaborate on the error you are seeing?
Thanks,
Greg Von Kuster
On Jun 10, 2014, at 8:07 PM, Vipin TS wrote:
> Hi Greg,
>
> When I trying to upload a next release version o my
> https://toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf converter program
> to Community To
Thanks for the contribution Carlos. The limitation that workflows only
can set one parameter be step is old at this point - the workflow API
definitely allows setting any number of parameters on any step - with
steps specified by individual step id or by tool id. This seems to
repeatedly trip peopl
Hi all,
I am working in a project that requires running workflows with multiple
parameter by using the Galaxy API.
However I realised that /api/workflows webservice does not allow to set
several parameters for one sigle step.
You can check that ingalaxy-dist/lib/galaxy/workflow/run.py
_update_
21 matches
Mail list logo
