It looks like the problem may have to do with the file I am using ???
It is a *.nii.gz file.
Does galaxy try to uncompress ? do something to *.gz files when using the api
(as it tries to do in ~/galaxy-dist/tools/data_source/upload.py
Does anyone know of where in the code I can edit so my mile
Further, it seems that it doesn't manage to get hold of the file specified in
the input directory as I can see from the output:
http://barium-rbh/csiro/api/histories/964b37715ec9bd22/contents/2faba7054d92b2df
{
"data_type": "html",
"deleted": false,
"download_url": "/csiro/datasets/
Hi,
I'm trying to get the example_watch_folder.py to run but it seems to fail,
and I'm not sure why?
I run:
./example_watch_folder.py 64f3209856a3cf4f2d034a1ad5bf851c
http://barium-rbh/csiro/api/ /home/galaxy/galaxy-drop/input
/home/galaxy/galaxy-drop/output "My API Import" f597429621d6e
Hello, Galaxy developers and maintainers!
I'm a user in Chinese mainland and I'd like to deploy our Galaxy server
locally. There's some requirements I cannot realize and I still have no
idea after searching over all Galaxy Wiki pages and Galaxy Developer docs.
The problem is, I need to jump from an
Howdy,
I am trying to install a tools shed item, Emboss, but when I do this
via the admin interface, I get the following text:
Repository installation is not possible due to an invalid Galaxy URL:
None. You may need to enable cookies in your browser.
I have searched the universe_wsgi.ini file an
Hi Kim,
We were able to resolve this in another thread, so am going to just
close this out.
Take care,
Jen
Galaxy team
On 4/30/13 5:50 AM, Kim Spradling wrote:
I have been trying to join the intervals of two datasets side-by-side
using the public Main instance, but the job never finishes. I'
Hello,
The public Main Galaxy server has been very busy this last week.
Hopefully most if not all of your work has completed by now, but if not,
the best strategy is to leave jobs running and not to stop/restart them.
If certain work is more urgent that others, run those first. Jobs are
exec
Hi Zain,
I believe we already worked out the .fastqsanger/grooming part of this
question in another thread. But for others reading this post, this is a
help link:
See "FASTQ"
http://wiki.galaxyproject.org/Support#Dataset_special_cases
Our RNA-exercise covers and example workflow:
https://main
Hi Carl, John,
Do you know if there has been any improvements regarding this issue?
As far as I know, the provided patch seemed to do the trick, although it
complicated the update to the latest Galaxy distribution a little bit (not
that much though).
I'm asking if there has been any finding on
Branden,
Thank you for reporting this issue, I've committed a fix in
9662:6c462a5a566d. You should be able to re-run your tool migration
after updating to that revision.
--Dave B.
On 5/7/13 11:09:31.000, Branden Timm wrote:
I recently upgraded to the latest galaxy-central, and was advise
Hi Peter,
On May 7, 2013, at 9:10 AM, Peter Cock wrote:
> On Tue, May 7, 2013 at 10:59 AM, Greg Von Kuster wrote:
>> Hi Peter,
>>
>> This change would be simple to make, but it would result in the inclusion
>> of all repositories with missing test components to be included in the list
>> of fa
Hi Bjoern,
It's good to know I'm not the only one to encounter this. I think it tends to
bite when you have alot of dependencies.
I use the same method as you (uploading one repo .. then another and so on) ...
using the script each time to automate the upload.
BTW I made a little addition
I recently upgraded to the latest galaxy-central, and was advised on
first run that two tools in tool_conf.xml had been removed from the
distribution, but could be installed from the tool shed. I ran the
script that it generated, however the script fails with the following
messages:
No handl
The current revision setting is treated as a minimum, so any available updates
are retrieved automatically at the time of installation. Even so, it may still
make sense to allow for a default of the latest installable revision if the
definition lacks a revision value.
Greg Von Kuster
On May 7
On Tue, Apr 30, 2013 at 2:04 PM, Dannon Baker wrote:
> Hey Dan,
>
> Sure, you can configure per-tool job runners. This wiki page
> (http://wiki.galaxyproject.org/Admin/Config/Jobs) should get you started,
> but let me know if you run into any trouble.
>
Thanks!
Following up on this.
As I menti
The text content is specified by the brand option in your .ini file.
For visual styles, you have the option of specifying a different
location for the CSS in your .ini file, with the static_style_dir
option. Note that if you're running behind a proxy configured to serve
static files directly,
On Tue, May 7, 2013 at 5:28 PM, Dave Bouvier wrote:
> Peter,
>
> I've updated the test tool shed with new code to also display (sandbox) in
> the page title attribute.
>
>--Dave B.
Thanks - that will help.
I've not looked how you did this, but ideally this text and the visual style
would be
Peter,
I've updated the test tool shed with new code to also display (sandbox)
in the page title attribute.
--Dave B.
On 5/6/13 14:11:10.000, Peter Cock wrote:
On Mon, May 6, 2013 at 9:55 AM, Peter Cock wrote:
On May 2, 2013, at 12:54 PM, Peter Cock wrote:
Another even simpler change
Hi Olivia,
Currently it's not possible to have conditional job execution in workflows,
though this is definitely something we've talked about adding.
The conditional toolbox element repository that you found is actually some
of John's work on conditionally having tools in the toolbox, not for
mak
Dear developpers,
I have a question concerning the insertion of conditions inside workflows ?
Here, at the pasteur Institute, we would like to use galaxy to create a
microbiome analysis workflow. However, it requires at least 10 different
tools which may be or may not be used in several cases.
On Tue, May 7, 2013 at 2:10 PM, Dave Bouvier wrote:
> Peter,
>
> As you've already noticed, I've tracked down and fixed the main issue that
> was causing inaccurate test results. Thank you again for the data you
> provided, which was of great help narrowing down the cause of the issue.
>
>--Da
Peter,
As you've already noticed, I've tracked down and fixed the main issue
that was causing inaccurate test results. Thank you again for the data
you provided, which was of great help narrowing down the cause of the
issue.
--Dave B.
On 5/7/13 04:50:23.000, Peter Cock wrote:
On Mon, Ma
On Tue, May 7, 2013 at 10:59 AM, Greg Von Kuster wrote:
> Hi Peter,
>
> This change would be simple to make, but it would result in the inclusion
> of all repositories with missing test components to be included in the list
> of failing tests. There are currently 2 filters that provide the
> info
On Tue, May 7, 2013 at 10:49 AM, Björn Grüning
wrote:
> Hi,
>
> nice work Ira! That problem also bothers me. I have written a similar
> script in python, but its not documented ;) I really think a more
> advanced solution like Peter's are needed midterm.
I've not written any code so its just an i
Hello Björn,
There is already a Trello card for this feature as I've been planning to
implement it for some time now (held up by bandwidth and other priorities).
I've added your comments to the card - thanks for the input!
https://trello.com/card/toolshed-enhance-the-current-galaxy-api-for-ins
Hi Ira,
that is a great new features, thanks!
Will try it soon.
Ciao,
Bjoern
> Hi Bjoern,
>
> It's good to know I'm not the only one to encounter this. I think it tends
> to bite when you have alot of dependencies.
>
> I use the same method as you (uploading one repo .. then another and so
Hello all,
during the last weeks the tool shed team did a lot of awesome work and
soon it should be possible to install meta-packages like Ira's
proteomics pipeline or the ChemicalToolBoX with a few clicks. Installing
all nested dependencies, datatypes and so on automatically.
One last problem I'
Hello Björn,
I've added your comments to the following Trello card. I'm doing some thinking
on this issue to make sure I come up with the optimal solution. Thanks for the
valuable input!
https://trello.com/card/toolshed-enable-dependency-definitions-across-tool-sheds/506338ce32ae458f6d15e4b3/
Hi Peter,
This change would be simple to make, but it would result in the inclusion of
all repositories with missing test components to be included in the list of
failing tests. There are currently 2 filters that provide the information to
categorize these repositories: missing test components
Hi,
nice work Ira! That problem also bothers me. I have written a similar
script in python, but its not documented ;) I really think a more
advanced solution like Peter's are needed midterm.
To fix the revision problems: What about leaving the revision tag blank
means that the toolshed should ins
On Mon, May 6, 2013 at 1:55 PM, Dave Bouvier wrote:
> Peter,
>
> Yes, there are a few issues that are causing some repositories not to be
> tested correctly. I've discovered the problem, but the solution will require
> a bit of work. My goal is to have this resolved as soon as possible.
>
>--D
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