Hi everyone,
I uploaded a bunch of files to the Galaxy data libraries with the option
Upload files from filesystem paths and Link to files without copying to
Galaxy. Afterwards I edited the names that are displayed in Galaxy. However,
now the files are not alphabetically sorted anymore. I
Hi Everyone
This is my first time on the mailing list. I am the administrator for a
production installation of Galaxy at Agriculture and Agri-Food Canada in
Ottawa, Canada.
Currently, I have a galaxy configured to start 3 web servers and 3 handlers.
When installing a tool from a toolshed,
I had the same concern, and heard that this is being worked on.
Meanwhile I’m using a rolling restart method from pjbriggs
https://github.com/pjbriggs/galaxy-admin-utils/
I’m pretty happy with this (desipite the 2 minute restart per worker) because
users do not see any interruption during
Hello Iyad and Brad,
Hello Iyad,
Yes, this is the current expected behavior.
There is a Trllo card here that tracks progress on this issue.
http://trello.com/c/B0pV80d0/1281-messaging-and-task-queue
This work is currently in progress with a baseline implementation available in
the upcoming
Thank you Greg and Brad,
That is a great tool (rolling restarts) and great news (working on
inter-process communication) !
Pardon my ignorance, but the rolling restart command refers to a manager,
web, and handler. What are Manager galaxy processes?
I've had issues where restarting all
Hello Jun,
See my answers inline.
On Wed, May 21, 2014 at 10:34 AM, Jun Fan j@qmul.ac.uk wrote:
Dear all,
I have a tool which generates dynamic number of mzid outputs
depending on the number of selected files and tools ( = number of files *
number of tools). The suggested
On Fri, May 23, 2014 at 9:07 AM, Greg Von Kuster g...@bx.psu.edu wrote:
I'm not quite sure whether this baseline implementation will handle
comunication between Galaxy web front-ends like you have (and like we have
for our public Galaxy instances).
Yep, it sure does. There's still a little
We have a pretty busy cluster, also SGE via DRMAA.
I do not notice jobs getting lost.
I did not notice that before switching to the rolling restart method either
though.
I have a vague memory of a config option to keep job state in the database …
not sure about that.
brad
--
Bradley W.
Hello all,
Large tabular data files in Galaxy are shown with auto loading,
meaning more data is loaded as you scroll down the page.
(As an aside, this can cause confusion, e.g. using CTRL+F to
search in the web browser would miss not-yet-loaded content.)
I've noticed with many BLAST tabular
Hey Peter,
By default, galaxy attempts to ship 50kb chunks of tabular data. It's a
good idea to probably support a minimum number of 'lines' to ship as well,
for text-based data -- I'll add a Trello card for this and will plan to
work on it soon.
That, and there should be an indicator along the
On Fri, May 23, 2014 at 2:42 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Peter,
By default, galaxy attempts to ship 50kb chunks of tabular data. It's a
good idea to probably support a minimum number of 'lines' to ship as well,
for text-based data -- I'll add a Trello card for this and
I am using the new_tool_panel_section_label option when installing
tools from the toolshed (via
scripts/api/install_tool_shed_repository.py. It works, but I'm curious
if its producing the wrong result.
See the attached image. I have installed a bunch of tools with
I notice that the galaxy web api for installing tools from the
toolshed does not include any entrypoint for uninstalling tools. This
must be intentional, but what was the motivation to leave this out?
Cheers,
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Hello Evan,
When installing tools into Galaxy from the Tool Shed, you are actually
installing Tool Shed repositories that contain tools, among other things (e.g.,
custom datatypes, exported workflows and other Galaxy utilities). The Galaxy
UI does provide the ability to unistall, but it is at
Hello Evan,
You're referring to an object we call a ToolSectionLabel, and I don't believe
that the Galaxy framework supports creating these objects automatically in real
time. You have to manually add them to one of your tool panel configs (e.g.,
tool_conf.xml, shed_tool_conf.xml, etc) via an
Hey Greg,
I see that option in the galaxy web UI, but I am working from the
command line and scripting against your toolshed web api. Its the api
that is missing the uninstall option for repositories/tools.
https://wiki.galaxyproject.org/ToolShedApi
Cheers,
-E
-Evan Bollig
Research Associate |
Hi Evan,
Sorry I somehow missed that in your original message - here is a Trello card
for enhancing the Galaxy API for the Tool Shed. I'll get to this as soon as I
can.
https://trello.com/c/4VktpvTd/207-enhance-the-galaxy-api-for-the-tool-shed-to-allow-uninstalling-a-repository
Greg Von
Dear Galaxy Developers,
I've been banging my head against this one for a few days now.
I have two Galaxy instances. One resides on a server called genomics, which
also hosts the corresponding PostgreSQL installation. The second also resides
on genomics, but its database is hosted on
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