I updated our wiki with this new build information.
https://wiki.galaxyproject.org/Develop/JSA
M.
On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler aysam.guer...@gmail.com
wrote:
Hi Christophe,
In order to apply the changes scripts have to be packed properly. Please
follow these steps:
1.
-developpement/genetique-et-epigenetique-de-la-drosophile
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05
Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50
christophe.antoniew...@upmc.fr
http://drosophile.org
2014-11-12 16:42 GMT+01:00 Martin Čech mar...@bx.psu.edu
The category Combinatorial Selections has been created on both Test and
Main ToolShed.
Thank you for your tool contributions Khalid.
Martin
On Mon, Oct 6, 2014 at 1:02 PM, Nicola Soranzo sora...@crs4.it wrote:
Hi Khalid,
I'd suggest you to open a Trello card for this:
Hi Chris,
(1) Galaxy configuration has been moved to /config/galaxy.ini
(
https://bitbucket.org/galaxy/galaxy-dist/src/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb/config/
)
(2) There might have been some changes to the conf syntax regarding the
dependency directory etc. since the version of
Seems like missing import:
from galaxy.model.orm import or_
I will check on it tomorrow as a whole.
Thanks for reporting this.
M.
On Tue, Oct 7, 2014 at 7:03 PM, Saket Choudhary sake...@gmail.com wrote:
I am trying to reset metadata on all my repositories at once using the
Reset metadata
somehow a space (escaped) got into your id
this is the correct url:
https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b5459666changeset_revisions=a54de7e658f7
I will look around why it got there.
On Tue, Sep 16, 2014 at 4:41 PM, Yves Gagnon
I tried installing this exact repo and changeset on the latest -central
galaxy code and encountered no problems.
What version of Galaxy are you using. Did you modify it?
Martin
On Tue, Sep 16, 2014 at 4:44 PM, Martin Čech mar...@bx.psu.edu wrote:
somehow a space (escaped) got into your id
I just freshly cloned galaxy-central, switched to next-stable and did
initial startup - no problems detected and Galaxy booted in under 2m.
On Tue, Aug 5, 2014 at 2:54 PM, Langhorst, Brad langho...@neb.com wrote:
I’ve noticed that startup is very slow.
It’s about 15 minutes for me to stop
There is a list of the ones that reached back to us and are publicly
accessible (~60): https://wiki.galaxyproject.org/PublicGalaxyServers
As of private ones there is no good clue as Galaxy does not call home.
M.
On Thu, Jul 24, 2014 at 12:55 PM, Lapointe, David david.lapoi...@tufts.edu
wrote:
file *api/authenticate.py*
class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ):
@web.expose_api_anonymous
def get_api_key( self, trans, **kwd ):
def get_api_key( self, trans, **kwd )
* *GET /api/authenticate/baseauth*
returns an
this answers that
question as well, thanks!
Cheers,
Eric
21.07.2014, 15:13, Martin Čech mar...@bx.psu.edu:
file api/authenticate.py
class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ):
@web.expose_api_anonymous
def get_api_key( self, trans, **kwd
chose one file in my computer to download.
I didn't use the character é in my e mail adress but I take into account
your advice !
Best regards,
Noémie
--
*De :* emulato...@gmail.com [emulato...@gmail.com] de la part de Martin
Čech [mar...@bx.psu.edu]
*Date
Hi Jun,
you can change any user's email through admin interface of Galaxy, no need
for SQL. You may break consistency when using SQL for changing users, which
might have happened to you.
best
Martin
On Fri, Apr 25, 2014 at 7:49 PM, Jun Fan j@qmul.ac.uk wrote:
Hi Martin,
Hi Jun,
Galaxy does not really delete users. If you are trying to clear the user,
just change its email as an admin and register the user again with the same
address as before.
Martin
On Thu, Apr 24, 2014 at 8:56 PM, Jun Fan j@qmul.ac.uk wrote:
Hi Martin,
Thanks for the hint.
Hi Moussa,
as Enis suggests please read the documentation and/or just call the API on
your local instance and see what it returns.
e.g. calling {{localhost}}/api/workflows?key={{API_key}} on my local
instance results in
https://gist.github.com/martenson/6b8e1d402fa193c914a5
Nice tool for
Hi Jun,
what kind of database are you using? This feature might not be supported
for SQLite (as no production Galaxy should run on it :))
best
Martin
Galaxy Team
On Thu, Apr 24, 2014 at 11:42 AM, Jun Fan j@qmul.ac.uk wrote:
Hi everyone
I followed the instruction at
Hi,
the place to start is the Reports app that comes with Galaxy, please see
the details here: https://wiki.galaxyproject.org/Admin/UsageReports
Martin
Galaxy Team
On Thu, Apr 17, 2014 at 5:06 PM, Alejandro Barrera
abarr...@biociphers.orgwrote:
Hi,
Apologizes if this is not the right place
Hello Xiaofei,
it seems you don't have username set in usegalaxy.org and thus the links
generated are wrong. Can you please set one (user/preferences/manage
information) and try again?
thanks
Martin
Galaxy team
On Fri, Apr 4, 2014 at 12:07 PM, Wang, Xiaofei xfw...@ku.edu wrote:
Dear there,
Hello,
it is great you want to share tools with others through Galaxy, thank you!
We call added software a 'Galaxy tool'. You can start by reading the tool
basics in this page: https://wiki.galaxyproject.org/Admin/Tools and then
you can browse through wiki where the vast of information about
,
Huayan
On Thu, Mar 20, 2014 at 10:27 AM, Martin Čech mar...@bx.psu.edu wrote:
Hello again Huayan,
the page got renamed and redirect was not in place. I have put it there
and the new page has even more info on it! :)
thank you for using Galaxy!
Martin
On Wed, Mar 19, 2014 at 10:18 PM
Hi,
I added your request to the card where we track these:
https://trello.com/c/mJWnAuuQ/1511-to-request-reference-genome-comment-on-this-card
Martin
Galaxy team
On Wed, Mar 26, 2014 at 3:17 PM, t...@caltech.edu wrote:
Hi Guys,
is it possible to add E.coli K12 genome for mapping with
Hi,
for installing tools into Galaxy please see the full guide:
https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy
for adding custom tools please see:
https://wiki.galaxyproject.org/Admin/Tools and
https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial
Martin
On Tue, Mar 25,
Hello Huayan,
I don't know why the wiki page disappeared and I will investigate it. In
the meantime I have found a cached copy for you:
http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+cd=1hl=enct=clnkgl=us
Martin,
Hello again Huayan,
the page got renamed and redirect was not in place. I have put it there and
the new page has even more info on it! :)
thank you for using Galaxy!
Martin
On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech mar...@bx.psu.edu wrote:
Hello Huayan,
I don't know why the wiki page
Hi,
Tool Shed was down today morning due to hardware relocation. It is up since
cca 3pm (EST) today. For up to date info about Galaxy including the
downtimes (both planned unplanned) please follow us on twitter.
https://twitter.com/galaxyproject
thanks for using Galaxy!
Martin
On Mon, Mar
Hello Shenwiyn,
the position of the menu items is defined by the order of these items in
the galaxy.menu.js file.
What do you mean by changing the galaxy interface?
Martin
On Mon, Mar 10, 2014 at 8:27 AM, Weiyan Shen shenw...@gmail.com wrote:
Hi Sam,
Using static/scripts/galaxy.menu.js,I
Awesome. How is the upload behaving? Are you still having issues with it?
M.
On Sat, Mar 8, 2014 at 12:20 PM, ruiwang.sz ruiwang...@gmail.com wrote:
Hi John,
Thanks for the note. Please see inline.
On Fri, Mar 7, 2014 at 7:18 PM, John Chilton jmchil...@gmail.com wrote:
Hmm... I am not
Hello Philip,
the page you are talking about should look like this:
https://www.dropbox.com/s/r97zvgl8a5h1u4z/Screenshot%202014-03-06%2017.07.52.png
How does yours look like?
Martin
On Thu, Mar 6, 2014 at 4:43 PM, Philippe Moncuquet
philippe.m...@gmail.comwrote:
Hi,
We have recently
Awesome, I am glad it is working for you.
Thank you for using Galaxy!
regards
Martin
On Thu, Mar 6, 2014 at 5:18 PM, steve.mcma...@csiro.au wrote:
Hi Philippe,
I realised we hadn’t restarted the reports application after the upgrade.
I’ve done that it seems to be working fine.
Dear Benoît Meilhac,
In my plugin, I would have to import the workflow, then run it with inputs
listed in the executable command line, and after a successful execution, I
would have to retrieve the outputs generated, then delete the created
workflow and any files related that exist.
The
Hello,
Björn has a point on the proper way to upgrade the Galaxy config file.
Please do not forget that you have to have your email server set up and
have Galaxy connected to it by changing the settings mentioned in the wiki
page. Without the server the activation will not be used even if
Hello Davide,
yes it does.
Also these two modifications of Galaxy might be if an interest to you as
they enhanced the sample tracking further:
http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/
Hi,
this has been resolved in galaxy-central repo (not dist). You can apply the
patch manualy, it is less than one-liner.
https://bitbucket.org/galaxy/galaxy-central/commits/3691fd3e12ef8160ae993cef5ebd51ddeee95da1
Martin
On Fri, Feb 14, 2014 at 1:28 PM, Nikos Sidiropoulos
Thank you Eric for the wiki page.
I agree that Galaxy Reports are not visible enough and this might help.
Martin, Galaxy Team
On Fri, Jan 17, 2014 at 12:29 PM, Eric Rasche rasche.e...@yandex.ru wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Well! This is the first I've heard of a
Hi Daniel,
I am sorry but Galaxy API doesn't support sharing of histories yet.
For further notice these two parts of the API documentation are the most
relevant for the histories API:
limitations in terms of file size,
no?
Would it be useable with large files?
Thanks,
Daniel
On 01/15/2014 07:05 PM, Martin Čech wrote:
Hi Daniel,
I am sorry but Galaxy API doesn't support sharing of histories yet.
For further notice these two parts of the API documentation
Hi,
I have tested user creation on local instance running galaxy-central and it
is running fine for me. Please se attached request and response
(printscreen from postman chrome extension):
https://www.dropbox.com/s/g7iiluq1tqc426p/Screenshot%202014-01-14%2014.22.45.png
Martin, Galaxy Team
On
Hi Nikos,
did you update your galaxy version recently? Did you use galaxy form
definitions at any time?
Martin
On Tue, Jan 14, 2014 at 8:30 AM, Nikos Sidiropoulos
nikos.sid...@gmail.comwrote:
I found the error in the logs:
Error - type 'exceptions.AttributeError': 'NoneType' object has no
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 Jan 3, 2014,
Hello,
to create a user through API you send a POST request to /api/users
More information about User API here:
https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.users
Martin
On Fri, Dec 27, 2013 at 5:11 AM, xlwang
are they in galaxy?
At 2013-12-18 12:13:58,Martin Čech mar...@bx.psu.edu wrote:
Hi,
the best start for using the API, that you found already, is the
documentation that, with a nice introduction, is nicely available here:
https://galaxy-central.readthedocs.org/en/latest/lib
Hi,
the best start for using the API, that you found already, is the
documentation that, with a nice introduction, is nicely available here:
https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html
Regarding libraries your main controllers of interest are: *libraries*,
Hi Sam,
you can reproduce this easily by going to Admin/Manage Data Libraries and
try to edit permissions for any of the existing library.
M.
On Wed, Nov 27, 2013 at 3:27 PM, sam guerler aysam.guer...@gmail.comwrote:
Hello David,
Could you provide more details on how to reproduce this i.e.
John just made it to the Wiki:
http://wiki.galaxyproject.org/Develop/SecurityToolTips
Feel free to add/edit/delete.
M.
On Thu, Nov 7, 2013 at 12:27 PM, John Chilton chil...@msi.umn.edu wrote:
Hello Ido,
The project has had a lot of contributors over the years, it is
probably not safe to
to the library, the formatting is
normal.
I'm assuming the fix is to just render the page before waiting for the
job to complete.
-Robert
On Nov 4, 2013, at 12:45 PM, Martin Čech mar...@bx.psu.edu wrote:
Hello,
I have also seen some of these errors while developing libraries. The
library code
Hello,
I have also seen some of these errors while developing libraries. The
library code is not in central however it might be related to recent
changes to the history panel. Carl Eberhard might now more, adding him to
the conversation.
--Marten
On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch
Hello Jordi,
user activation feature and other features described at the page you
mentioned are implemented and part of the development galaxy-central (
https://bitbucket.org/galaxy/galaxy-central) repository. However they are
not yet part of the official release repository (galaxy-dist -
Hello David,
please see whether Data Libraries (
http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries) with the file
import (
http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles)
and especially the *Upload files from filesystem paths* feature do solve
your problem. It
Hi Adam,
you are right about the behaviour, this is what Galaxy does. However it
sends the email to the user too, so Reply all will reach the user's email
address. This is how the feature was meant to be used.
Martin
On Tue, Oct 1, 2013 at 12:59 PM, Adam Brenner aebre...@uci.edu wrote:
of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu
On Tue, Oct 1, 2013 at 10:52 AM, Martin Čech mar...@bx.psu.edu wrote:
Hi Adam,
you are right about the behaviour, this is what Galaxy does. However it
sends
. That was a pretty stupid mistake, hard to notice
even though I program in Python.
However, this has not solved my problem, I get the same error. (I have
also made sure that it is in the right section.)
Jan
2013/9/25 Martin Čech emulato...@gmail.com
Ahoj Honzo,
Python is case-sensitive. Use
Ahoj Honzo,
Python is case-sensitive. Use 'use_pbkdf2 = False' and make sure you put it
under the '[app:main]' section in the config file.
Enjoy Galaxy!
best
Martin Cech
On Wed, Sep 25, 2013 at 9:15 AM, Jan Hapala j...@hapala.cz wrote:
Hi,
I need to run Galaxy with ProFTPd, therefore I
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