Hi guys,
I have several jobs have been stuck in the queue for long time, I checked
the handler log and found the following message:
Job runner assigned but no external ID recorded, adding to the job handler
queue
Is there a way that I can clean these orphan jobs out of the queue?
Cheers,
Derric
Hi, Lee - the last line of that error dump might be worth thinking about.
It seems clear enough. Your python interpreter seems unable to import a
module called yaml
Perhaps you need to (eg) do
pip install yaml
in the virtualenv (or sudo ... for the system one if not using a
virtualenv) you're runn
Hi,
I am trying to integrate a tool that is written in java into galaxy. The
following is what I've done.
1) Created a directory inside /tools directory and put my xml and runnable
jar file in it.
2) Linked the xml file in 'tool_conf.xml'.
*tool_conf.xml*
*sample.xml*
I am trying to install Galaxy on a new iMac (i7, 32gb ram, OSX 10.8). Mostly
the install worked and I can use my local install. However, about 25% of the
functional tests failed for me. And about 4 of the unit tests failed for me.
Also, I can't seem to install anything from the toolshed (logged
Hi all,
I am trying to integrate a tool written in java into galaxy. The java
code will output a GUI window.
I want to know how to output that window in the middle pane
Thanks,
VJ
___
Please keep all replies on the list by using "reply a
The web process is definitely the bottleneck right now, creating more
should improve things. I'd guess it wouldn't speed up any individual
submission, but it'd allow you to submit several at once. Lastly, this is
a known issue that we're hoping to resolve with a rewrite of the workflow
dispatchin
Hi all,
I am trying to integrate a tool written in java into galaxy. The tool
opens a GUI window to output a graph and also writes a text file.
I want to know how to output that graph in the middle pane and
how to output the text file so that the user will be able to download
it.
*Sample
Hi,
I am routinely running hundreds of pair-end sequencing runs and find that
STARTING a workflow on all of these can easily take hours since it seems
each workflow preparation takes about 3 minutes, so for doing 128 fastq
pairs like this it will take over 3 hours just to get all workflows
runn
>>
>> sample.xml
>>
>>
>>java -jar sample.jar
>>
Your tool config does not define any output elements, so no dataset is
created. You need to define at least one output, and then use it's
name in the command line.
__
Hi,
>
>I am trying to integrate a tool that is written in java into galaxy.
> The following is what I've done.
>
> 1) Created a directory inside /tools directory and put my xml and runnable
> jar file in it.
> 2) Linked the xml file in 'tool_conf.xml'.
>
> *tool_conf.xml*
>
>
>
>
>
Initially only one volume is shown on Amazon's EC2 management console. Then,
after the user goes into the instance's URL and logs into Cloudman, they are
prompted with a box called "Initial cluster configuration" where they specify
the size of the volume they want. THEN, three nameless volumes a
Hello again,
I guess I now realize why there is so much traffic on the user list about
tools, and I also can guess that while the online directions for dealing
with them are written well for those individuals familiar with
administration a server or doing full time bioinformatics, but there are
so
Hello Joachim,
What version of Galaxy are your running?
What does the tool shed paster go show for the 500 Internal Server Error?
Also, run the following sql manually in your Galaxy database and send the
results.
select id, tool_shed, name, owner, installed_changeset_revision, status,
err
Hi all,
I have developed a tool in our local Galaxy, and imported it in a local
toolshed. I next removed the 'dev' version of the tool in Galaxy, and
installed it now via het Tool Shed Manager.
I got an error that the dependencies could not be installed. If figured it
out that it (needed to add a
Hi, I am running into an error that I bet has a simple solution. I would
appreciate any help. Thanks.
I am running Brad Chapman's LIMS extension locally on Ubuntu 12. I also
installed it as a service under /etc/init.d/chapman-galaxy using
contrib/galaxy.debian-init . It works when I run it dire
You'll need to wait until the history is ready for download -- i.e., Galaxy
provides a .gz file rather than a Webpage at that URL -- before using wget.
Galaxy returns a webpage (text/html) while preparing the history for download;
this is likely what you are downloading now.
Good luck,
J.
On
Hi Peter,
We edited the ncbi_blastn_wrapper.xml (attachment) a little bit as you can see
and created a taxid_name.loc file for testing by our own. This is what we were
thinking of in a very simple way. But if the list spreads out we would like to
have textbox for pre-selection above the drop-do
Hi all,
I have developed a tool in our local Galaxy, and imported it in a local
toolshed. I next removed the 'dev' version of the tool in Galaxy, and
installed it now via het Tool Shed Manager.
I got an error that the dependencies could not be installed. If figured
it out that it (needed to
18 matches
Mail list logo
