On Mon, May 6, 2013 at 1:55 PM, Dave Bouvier d...@bx.psu.edu 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.
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
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
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!
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
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 on)
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!
On Tue, May 7, 2013 at 10:49 AM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de 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
On Tue, May 7, 2013 at 10:59 AM, Greg Von Kuster g...@bx.psu.edu 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
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,
On Tue, May 7, 2013 at 2:10 PM, Dave Bouvier d...@bx.psu.edu 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.
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
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
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 p.j.a.c...@googlemail.com wrote:
On May 2, 2013, at 12:54 PM, Peter Cock wrote:
On Tue, May 7, 2013 at 5:28 PM, Dave Bouvier d...@bx.psu.edu 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
On Tue, Apr 30, 2013 at 2:04 PM, Dannon Baker dannon.ba...@gmail.com 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
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
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
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 g...@bx.psu.edu 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
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
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
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:
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.
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
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
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
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:
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