Hi Philip
The appearance of the visualization button depends on the datatype of
your output. E.g. when it is set to 'tabular', you should get the button
allowing you to create a scatter plot.
However, depending on your data, it might not make much sense to
visualize it in 'Trackster',
Hi,
For testing I have installed custom tool A and its repository dependency
custom tool B. Actually as per the implementation there is no dependency
among these two custom tools. But in general if we want to access a tool
inside another tool implementation how should I do that.
Can you please
Hi,
I used the torque/pbs system with Galaxy
In the newer stable version (2014.2.10), the PBS job did not stop when I
deleted the running dataset.
It can be deleted with such API:
http://127.0.0.1:8080/datasets/f2db41e1fa331b3e/delete_async
Seems the js did not work?
Regards,
Jian-Long
Hi Jen,
I tried what you explain, but still doens't work.
I did create a new datatype, gem. And I modified my code as you suggested.
The tool i'm using always generates by default two archives . gem and .log.
Those are the ones that I can't show in the galaxy interface, the output I
get is empty,
Hello Carrie,
I put an artificial sleep into upload.py and tried to replicate this
with the local, DRMAA, and SLURM job runners but could not. I was
working out of galaxy-central instead of galaxy-dist s it is possible
it has been fixed since the last dist update - the history panel has
seen a
On Sat, Apr 5, 2014 at 8:07 AM, ANGELICA GOMEZ ROIG
nirvanargr2...@gmail.com wrote:
Hi Jen,
I tried what you explain, but still doens't work.
I did create a new datatype, gem. And I modified my code as you suggested.
The tool i'm using always generates by default two archives . gem and .log.
Just to add to what Peter said - you definitely don't want to use
from_work_dir and reference the outputs ($output1) in the same
command. If you know where the file is going to be relative to your
working directory there should be no reason to pass it to your script.
Also I think you want format
Yes, there was a bug in the latest release that was fixed by Nate
after the release. Full details are available in this thread:
http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-tt4663719.html
-John
On Sun, Apr 6, 2014 at 2:24 AM, Jian-Long
Hi,
we recently activated the feature for non admin users which allows them to
upload a directory of files:
...
# Add an option to the library upload form which allows authorized
# non-administrators to upload a directory of files. The configured directory
# must contain sub-directories named
I think you need to hack up the Galaxy code to accomplish this. There
is information on how to start doing this in the following thread I
think:
http://dev.list.galaxyproject.org/FTP-Problem-Users-cannot-see-their-uploads-files-tp4619709p4662701.html
This may just work for admin users though, I
Hi Daniel,
Would you be OK with me/us incorporating your example
Galaxy Data Manager [1] for NCBI BLAST databases
http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blastdb_ncbi_update_blastdb
into the Galaxy BLAST wrappers repository
https://github.com/peterjc/galaxy_blast/
Hi Nate,
I have waited for all 3 instances of dataset 301 in history_dataset_association
to be older than 30 days. Then I re-ran the admin script. As expected all 3
instances now have TRUE as there deleted status. I then tried the following
commands as you suggested:
python
Hi Peter,
It would be great to have the BLAST tools use tool data tables and Data
Managers. Let me know what I can do to help.
Thanks,
Dan
On Apr 7, 2014, at 11:48 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Daniel,
Would you be OK with me/us incorporating your example
Galaxy
On Mon, Apr 7, 2014 at 5:38 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Peter,
It would be great to have the BLAST tools use tool data tables and
Data Managers. Let me know what I can do to help.
Thanks,
Dan
That's great Dan - I see you've commented on GitHub, so we can
continue this
Hi John,
thanks for your reply, I'll give it a try.
Thomas
Von: John Chilton [jmchil...@gmail.com]
Gesendet: Montag, 7. April 2014 16:15
An: Berner, Thomas
Cc: galaxy-dev@lists.bx.psu.edu
Betreff: Re: [galaxy-dev] authorize non admin user to only link a
Hey folks! I'm trying to revise a tool that allows the user to select from an
extendable list of template files for generating blast report output. The idea
is that if some reporting needs aren't covered by a generic template, then they
can develop their own template which can then show up on
Isn't this how *.loc.sample files already work? If there is
no pre-existing *.loc file, the *.loc.sample file is copied
to become the initial *.loc file which the local Galaxy
administrator can update/fill in as needed.
Peter
On Mon, Apr 7, 2014 at 9:39 PM, Dooley, Damion damion.doo...@bccdc.ca
Oh, great! I'd assumed new tool versions would overwrite them so they could
implement changes. But what you say is simpler and more straightforward!
Thanks,
D.
From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Monday, April 07, 2014 2:23 PM
To:
Galaxy admins, a couple questions:If you're running galaxy with REMOTE_USER authentication, do you have local users on the same box?If you do, have you done anything to mitigate administrator impersonation in galaxy?We currently have galaxy deployed on a box that acts as a classroom server. I was
Hi Rudolph,
Thanks for the answer. I understand that it would make no sense to allow
generation of graphics on non relevant data. My data is in tabular format
and that is the reason why I was surprise not to see that button.
outputs
data name=tabular_file label=report.tsv type=tabular
I’m running with these local additions to Dannon’s metaphlan repo.
I think it would be better to add these to the current metaphlan repo than to
release them standalone.
metaphlan_to_krona.xml
Description: metaphlan_to_krona.xml
#!/usr/bin/env python
#
This patch updates bjorn’s bismark wrapper to work with latest bismark and
allows methylation extraction from SAM or BAM files.
It no longer sorts the BAM from bismark (to allow methylation extraction to
work).
bismark_patch.diff
Description: bismark_patch.diff
Comments/corrections
Hi
When selecting a file or after clicking on Execute to upload a file is it
possible to check the file is appropriate i.e. by checking file extension etc,
before the file is actually uploaded and put into the database? So the user
can't upload the wrong file/format
Thanks
Neil
Neil
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