/job_conf.xml.sample_advanced ), but this
would define the environment variable also for all the other tools
that use that destination (normally not a problem, but worth to mention).
Cheers,
Nicola
On 05/05/18 15:04, Evan Clark wrote:
Have you ever seen this error with export to cluster
Has anyone attempted to write a tool that allows copying of galaxy
datasets locally, i.e. without downloading via http. We have scenario
where there are some additional tools available only via command line
and it would be very useful to be able to directly copy galaxy datasets
from the
Is it possible to execute a script within a tool xml confit to retrieve some
data and append to the ui depending on the requested data. I.e if I wanted to
get a list of files and provide them as select options before hitting the
execute button.
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When using the upload tool on our local galaxy we are experiencing an
issue with tool factory pointing to the incorrect directory. Below
dhouldn't be /var/web_services but rather /mnt/ceph/.
We are unsure how to change it our how to fix this issue.
Traceback (most recent call last):
Is there a way to change the location of the galaxy lib directory? We
migrated our galaxy and it is looking for the lib on the wrong location.
Additionally this is causing errors like the one below the first error.
galaxy.jobs.runners DEBUG 2017-09-01 09:35:13,673 executing external
set_meta
I have been testing our new galaxy instance and came across an odd
issue. When a user is logged in and attempts to set their preferences
the view does not render and the galaxy UI is inset in the center
section. This also occurs when clicking public name. No errors are shown
in the log. See
Yes I installed flask and the other prerequisites.
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When attempting to start the galaxy communication server with all
dependencies installed we receive the error below.
(.venv)[galaxy@galaxy galaxy]$ python
./scripts/communication/communication_server.py --port 7070 --host 127.0.0.1
Traceback (most recent call last):
File
We are setting up galaxy with the new files directory option enabled so
that our instance will run jobs from our scratch. We are curious to know
if galaxy itself copies the final output files directly to our files
directory or if this occurs within the scope of a cluster node running a
job.
I just ran across an issue when attempting to load galaxy. I am not sure
how to fix this issue or what could be causing it. Conda is installed
properly.
File
"/var/web_services/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line
58, in paste_app_factory
app =
I remember there previously being an additional tool that ran on a
different port from galaxy that allowed for monitoring of performance
and jobs running. Is this tool still packaged with galaxy and if so how
can it be activated.
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Has anyone ever encountered an error such as this when running galaxy
with slurm and submitting files for upload and unzip.
slurmstepd: get_exit_code task 0 died by signal
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That may work, but now we are getting this error.
Exception happened during processing of request from ('127.0.0.1', 43030)
Traceback (most recent call last):
File
"/cm/shared/apps/galaxy/prod/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py",
line 1085, in
Has anyone seen a similar error like this before. We are unsure if
galaxy is causing the issue or it is being cuased by slurm as it seems
galaxy is prematurely deleting a file.
galaxy.jobs.runners DEBUG 2017-06-14 19:36:45,719 (3261/143577) Unable
to cleanup
Is there a method to setup a command to run depending on the filetype of
a job. Essentially I want to setup a task where everytime a bedgraph
file is generated it will either automatically start a new job and
convert it to bigwig or, within the same job file it will convert the
bedgraph to
I am setting up a new galaxy instance and upon intial setup and user
login I get this error. The database is brand new and there is no data
in any history as I am the sole user at this moment.
"onLine": true,
"version": "17.05",
"xhr": {
"readyState": 4,
"responseText":
Is there a script someone has designed to properly dump the galaxy
sqlite database to a mySQL database?
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I connected our galaxy instance to mariadb with no connection issues and
it began to migrate the data, I noticed however when galaxy was finally
started the tables were generated, but no data was migrated. It
completed the migration without error so I am not sure if there is a
setting I missed
Yes, these alignments were done to ensemble, not UCSC.
---Regards, Evan Clark
Reminder: If this message is requesting you to verify your account or provides
links for you to login to your account, you are advised to ignore such
requests. Neither FAU nor legitimate financial institutions
Is there a good method for moving a fully functional galaxy install from
one machine to another in a different directory?
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Our production instance has been connected to apache for external
authentication. What we would like to know if there is a method to run a script
after a users initial login to generate a folder with their email in the file
upload location.
---Regards, Evan Clark
I am unsure as it does compile properly outside of galaxy. How do I
check these and make sure they are the same?
Nate Coraor <mailto:n...@bx.psu.edu>
October 31, 2016 10:25 AM
Are your libX* libraries and headers the same version?
evan clark <mailto:eclar...@fau.edu>
October 31
angerous,
better use `mkstemp'
/usr/lib/../lib64/libXext.so: undefined reference to `_XEatDataWords'
collect2: error: ld returned 1 exit status
make: *** [bin/gs] Error 1
Nate Coraor <mailto:n...@bx.psu.edu>
October 31, 2016 10:12 AM
Hi Evan,
Can you include the full error you're receivin
I was installing a tool from the galaxy toolshed and one of the
dependencies was missing due to a bad link. I modified the install files
to use the same version of the the software except from a local
directory, however galaxy renders a large error when compiling. If I
compile the source in
I have written the below tool wrapper and when running in galaxy I
receive the error. I am not sure the issue with the wrapper.
Traceback (most recent call last):
File
"/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py",
line 170, in prepare_job
I am currently working to create a wrapper for the MISO tools and wanted
to see if anyone has previously developed a functional or
semi-functional wrapper for it.
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I have modified the shed tool conf xml in order to add labels to tool
sections and it appears to now be reading the xml in reverse and
ordering the tools in the tool panel incorrectly.
Image of issue:
I am setting up a production galaxy server and am having an issue with
running HISAT 2. It appears that it is not able to find samtools and
renders an error within galaxy. Below is the error that it produces. I
am unsure how to get the full error log for HISAT.
|Traceback(most recent call
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