Hello Damion,
I believe this issue was corrected in
https://bitbucket.org/galaxy/galaxy-central/commits/3d8841746ce9b65e19a44028dea2eac73a4eddf8
It looks like you are tracking the galaxy-central brach, so if you pull and
update your repository you should get the fix.
Greg Von Kuster
On Jan
A few of our local galaxy installs have a relative folder path (i.e. in
universe_wsgi.ini, "prefix = /galaxylab") . In the Admin tab, "Manage
installed tool shed repositories", the icons in the legend below aren't showing
because they have an absolute url:
I can see in the
galaxy-central/l
Hello Elsayed,
Your protocol below seems to be a mix of a variant detection and an
RNA-seq workflow. To build a workflow for RNA-seq, you will want to
compare your steps with the protocols in the link that I sent you.
If you want more examples, many more can be found here (for both RNA-seq
a
Works like a charm without the single quotes. Thanks for the help.
Prakash
On Jan 3, 2014, at 2:50 PM, Nate Coraor
wrote:
> In universe_wsgi.ini, remove the single quotes from the value of
> remote_user_header, e.g.:
>
>remote_user_header = HTTP_AUTH_USER
>
> If that doesn't fix it, plea
In universe_wsgi.ini, remove the single quotes from the value of
remote_user_header, e.g.:
remote_user_header = HTTP_AUTH_USER
If that doesn't fix it, please make sure you don't have local changes
interfering, e.g. inspect `hg diff`.
--nate
On Fri, Jan 3, 2014 at 2:21 PM, Velayutham, Prakas
I know a few people have talked about using docker to package and
distribute Galaxy tools. The most recent version now runs on all major
linux distributions, so it's a bit more inclusive now (but there probably
won't ever be a windows or mac version). One strategy would be for tool
configs to defin
[srv-galaxy@bmigalaxyp1 galaxy-dist]$ hg summary
parent: 11939:e92e13e9c103 tip
Allow changing the header for remote user.
branch: default
commit: 1 modified, 1 unknown
update: (current)
[srv-galaxy@bmigalaxyp1 galaxy-dist]$
Prakash
On Jan 3, 2014, at 2:11 PM, Nate Coraor
wrote:
> Hi Prakash,
Hi Prakash,
Could you send the output of `hg summary`?
Thanks,
--nate
On Fri, Jan 3, 2014 at 1:41 PM, Velayutham, Prakash (Prakash)
wrote:
> Hi Nate,
>
> I just updated my copy and the changes you pushed are in. However, the auth
> part is not working still. I added
>
> remote_user_header = 'HT
First of all, best wishes!
I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu
system. However I stumbled upon an issue were it remained grey. When I did
an automaic visualization I saw a line that went up and down over the
chromosome. When I switched to pack I got a grey /
OK, got it. Pulling galaxy-central now. Will let you know.
Thanks,
Prakash
On Jan 3, 2014, at 12:22 PM, Martin Čech
mailto:mar...@bx.psu.edu>>
wrote:
Prakash: not unless your default pull is galaxy-central repository.
M.
On Fri, Jan 3, 2014 at 11:49 AM, Velayutham, Prakash (Prakash)
mailto
Prakash: not unless your default pull is* galaxy-central* repository.
M.
On Fri, Jan 3, 2014 at 11:49 AM, Velayutham, Prakash (Prakash) <
prakash.velayut...@cchmc.org> wrote:
> Hi Nate,
>
> If I do a "hg clone" of my default pull, this should already be there?
>
> Thanks,
> Prakash
>
> On J
Hi Nate,
If I do a "hg clone" of my default pull, this should already be there?
Thanks,
Prakash
On Jan 3, 2014, at 11:45 AM, Nate Coraor
mailto:n...@bx.psu.edu>>
wrote:
Hi Prakash,
This was not previously possible, but I have added a config option for it:
https://bitbucket.org/galaxy/g
Hi John,
I think I found the issue. I had not commented out the "cookie_path" directive
which is what caused the HISTORY issues I saw. However, I still would like to
know if Galaxy can take something other than REMOTE_USER in the header variable
to do external authentication.
I would much rath
Hi Prakash,
This was not previously possible, but I have added a config option for it:
https://bitbucket.org/galaxy/galaxy-central/commits/e92e13e9c103cc1f36dff65e1523479bf5cb17ed
If you're running the stable branch, you can apply the changes from this
commit manually.
--nate
On Thu, Jan 2,
I have created a Trello card for this request here -
https://trello.com/c/Fk1mcGnZ.
-John
On Thu, Jan 2, 2014 at 11:48 AM, Thon deBoer wrote:
> Absolutely!
>
> As long as I don’t need to open up the XML file in the toolshed tree…
>
> Regards,
>
> Thon
>
>
>
>
> On Dec 31, 2013, at 11:53 A
Can you set a more specific datatype? This is a hack from a heavy
Galaxy user and developer:
"What I and others are doing is hacking the library file path uploads
functionality. If you upload by file path, select your compressed
fastq files, and set data type to fastqsanger (*this is the key
step*
I am not sure I understand the problem. Can you clarify a few points:
Is bioblend letting users associate roles with data libraries that
they shouldn't be able to and the operation is succeeding -or- are you
trying to add roles and the operation is failing?
If the API is producing an error messag
Do you have a diff for the Galaxy changes you made? I could provide a
second set of eyes to try to figure out if there is something you
missed.
I would guess the best way to handle this would to have Apache
translate whatever is coming from your Oracle product into a
HTTP_REMOTE_USER header - my i
Hello Jen,
For this problem, you will need to reach the support or administrators
for this public server.
https://wiki.galaxyproject.org/PublicGalaxyServers#ODoSE
The authors of the primary publication are probably the best contacts (I
couldn't locate any others). You can find these linked fr
Hi,
We have a SSO environment provided by Oracle Fusion products and for some
reason, they don't like to send over HTTP_REMOTE_USER as a header variable to
downstream servers. I have seen it before with other web sites I have
integrated with Oracle Access Manager. Is there a way Galaxy can acce
Hello to all,
I'm trying to use the function "/upload_file_from_server/" from the
galaxy libraries api of Bioblend.
It's working correctly when i don't associate any role to the arguments.
However, in our architecture (Institut Pasteur, Paris) it can't be
possible that any user may upload a
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