Can I throw in a bounty for this one? ;-)
On 18 April 2014 03:09, Saket Choudhary wrote:
> John pointed out that the error its the upload of the test file itself
> which is failing. I can locate the input files
> in test-data/
>
> https://travis-ci.org/saketkc/galaxy_tools/jobs/23238748#L1723
>
There's a built in reporting webapp
See https://wiki.galaxyproject.org/Admin/UsageReports
Cheers
Eri
On April 17, 2014 2:07:56 PM CDT, Alejandro Barrera
wrote:
>Hi,
>
>Apologizes if this is not the right place to ask this sort of
>questions, but I have been asked to report user usage in our l
Hi,
my tool needs both a file with chromosome lengths and the total mappable genome
size.
I would like to hardcode the mappable genome size per build somewhere.
However the user should have to use only one drop down to select both. How can
I achieve this?
e.g. currently:
Hi,
I am having a problem with updating our local Galaxy server, and I am hoping
someone can help me.
Yesterday I performed a 'hg incoming' command. A bunch of updates were
applied, from changeset 12443:ec9d31a8bc04
to changeset 13068:c05752549163. I restarted the server (in daemon mode), bu
Hi,
Apologizes if this is not the right place to ask this sort of questions, but I
have been asked to report user usage in our lab’s instance of galaxy. In order
to crunch the numbers by user (number of logins per month, number of jobs,
memory usage, etc.), I thought that in principle, I could
Galaxy has a fantastic developer community, from the very active mailing
lists and #galaxyproject IRC channel to individuals who have submitted
literally hundreds of pull requests and patches. We are always looking for
ways to interact with existing community members and get even more people
invol
John pointed out that the error its the upload of the test file itself
which is failing. I can locate the input files
in test-data/
https://travis-ci.org/saketkc/galaxy_tools/jobs/23238748#L1723
Any clues as to where exactly am I going wrong?
On 17 April 2014 19:40, Saket Choudhary wrote:
> Ap
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
wrote:
> Hi,
>
> Apologizes if this is not the right place to ask this sort of
Hi,
Apologizes if this is not the right place to ask this sort of questions, but I
have been asked to report user usage in our lab’s instance of galaxy. In order
to crunch the numbers by user (number of logins per month, number of jobs,
memory usage, etc.), I thought that in principle, I could
I saw the same phenomenon. I think it stems from the current version of
compute_q_values pointing to unavailable revisions of both R and the
bioc_qvalue R package. Whoever maintains the compute_q_values needs to
straighten out the revision ids.
David Hoover
Helix Systems Staff
National Instit
Hi,
I am having a problem with updating our local Galaxy server, and I am hoping
someone can help me.
Yesterday I performed a 'hg incoming' command. A bunch of updates were
applied, from changeset 12443:ec9d31a8bc04
to changeset 13068:c05752549163. I restarted the server (in daemon mode), bu
This API controller broke with the latest release from earlier this
week - I have since fixed this in galaxy-central and opened a pull
request to have it fixed in the stable branch. Otherwise I think it
was worked for quite some time. The bioblend commands should be
something like this...
>>> gi =
On Wed, Apr 16, 2014 at 12:16 PM, Dooley, Damion wrote:
> Thanks for your input, John. I see, so from what you say, anything installed
> via pip in the virtual environment then exists in the module/class include
> namespace within galaxy python command line tool code. Good to know.
>
> I'll no
Hi,
my tool needs both a file with chromosome lengths and the total mappable genome
size.
I would like to hardcode the mappable genome size per build somewhere.
However the user should have to use only one drop down to select both. How can
I achieve this?
e.g. currently:
My attempt to 'package' pycurl on testtoolshed fails with the following error:
src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15:
warning: call to ‘_curl_easy_getinfo_err_string’ declared with
attribute warning: curl_easy_getinfo expects a pointer to char * for
this info [enable
Apparently my tool itself does a web API call, so the test is bound to
fail locally. My best bet is to rely on travis for now, however I
still see this failing:
https://travis-ci.org/saketkc/galaxy_tools/jobs/23206181#L1721
The input file exists:
https://travis-ci.org/saketkc/galaxy_tools/jobs/232
This is a good idea, and I’ve implemented it in this -central changeset:
https://bitbucket.org/galaxy/galaxy-central/commits/c055181847a46dc3199458d899d28d559ae43c38
If you’re working with galaxy-dist, you can pull this one changeset and use it
until the next release. Let me know if you have any
HI John, Saket,
Looking at Skaet's .travis.yml he doesn't mess about with the
default datatypes_conf.xml(.sample) like I do, so his TravisCI
should have all the default Galaxy datatypes (including tabular).
In my more complex .travis.yml I modify this to two reasons,
first to add new datatypes, a
Culprit: System Proxy.
I am behind a proxy and have my http_proxy, https_proxy variables set.
The trick is to unset them.
Because I am relying on John's template[1] for testing, I had to just
unset http_proxy ONLY.
Maybe I should add this to the wiki?
[1]
https://github.com/jmchilton/galaxy-d
Hi, Saket - 436 tests in 19.153 seconds means something odd (or fast) with
your setup?
What errors do you see?
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4J
On Thu, Apr 17, 2014 at 10:43 PM, Saket Cho
Oppps, duh sorry I thought condel_input.tabular was a datatype not a
file. That makes sense. I'll look some more.
-John
On Thu, Apr 17, 2014 at 7:45 AM, Saket Choudhary wrote:
> Hi John,
>
> My tool's input datatype is tabular. I do not have any custom datatypes
> defined.
>
> Saket
>
> On 17 A
Hi John,
My tool's input datatype is tabular. I do not have any custom datatypes defined.
Saket
On 17 April 2014 18:10, John Chilton wrote:
> I don't see anywhere in your Travis YAML file where you are modifying
> Galaxy's datatypes (like Peter does for instance on these lines
> https://github.
Just to add, that is the case with all the tests:
$ sh run_functional_tests.sh
Ran 436 tests in 19.153s
FAILED (errors=434)
All tests fail locally and hence I decided to rely on travis.
https://wiki.galaxyproject.org/Admin/RunningTests#Functional_Tests
says it might be due to conflicting version
I don't see anywhere in your Travis YAML file where you are modifying
Galaxy's datatypes (like Peter does for instance on these lines
https://github.com/peterjc/pico_galaxy/blob/master/.travis.yml#L166).
If those datatypes are not defined you cannot upload a tool with a
specific type. Am I missing
On 17 April 2014 15:34, Peter Cock wrote:
> On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary wrote:
>> I happened to copy Peter's .travis.yml for running tests for some of
>> my packages.
>
> Background information:
> http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-to
Hello,
I am developing a web application, where I want to show a Trackster
visualization in an iframe from our local Galaxy Server.
The problem is that I am not able to specify over a locus via the URL
when I am not the owner of the visualization.
(When we click "saved Visualization" we can spe
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary wrote:
> I happened to copy Peter's .travis.yml for running tests for some of
> my packages.
Background information:
http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-tools.html
> However the process has not been smooth
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