Dear all,
We have a modified Galaxy server with tools for virtual screening. You can
access is at http://lisis.cs.ucy.ac.cy.
We created a composite datatype (auto_primary_file) to handle PDBQT files
for proteins and their config file requested by AutoDock Vina, in simple
words is a composite
Hi Team,
I am working on setting up a Cloudman instance for a course we are preparing.
I have used the link provided: http://usegalaxy.org/cloudlaunch and can get an
instance running. The issues are as follow:
1. I need to add tools and have not found a clear method in doing so utilizing
On Fri, Mar 22, 2013 at 8:40 AM, Iry Witham iry.wit...@jax.org wrote:
I am working on setting up a Cloudman instance for a course we are
preparing. I have used the link provided: http://usegalaxy.org/cloudlaunch
and can get an instance running. The issues are as follow:
1. I need to add
Hi guys,
I'm wondering whether it is possible to have user-specific tool panels after
logging in. This way users could customize the tool panel for instance by
increasing the visibility of their (user-specific) favorites ... This would be
a wonderful feature.
However searching in the
Hi Dan,
I just updated our sources and… it works !
Thanks a lot,
Regards,
Julien
Le 21 mars 2013 à 16:30, Daniel Blankenberg
d...@bx.psu.edumailto:d...@bx.psu.edu a écrit :
Hi Julien,
This was fixed in changeset 6cd4058d7b32
I have been running a Galaxy server for our sequencing researchers for a
while now and it's become increasingly successful. The biggest resource
challenge for us has been, and continues to be disk space. As such, I'd
like to implement some additional cleanup scripts. I thought I run a few
On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote:
I have been running a Galaxy server for our sequencing researchers for a
while now and it's become increasingly successful. The biggest resource
challenge for us has been, and continues to be disk space. As such, I'd like
to implement
Hi Vipin,
Thank you for reporting this issue.
This has to do with the way that the old-style (hard-coded) display
applications were modified after introduction of roles to authorize access to
an user's datasets that might be permission protected.
Ideally, with these old-style applications,
Glad that everything works now for you. The Get Updates functionality
won't work since this is a new version of the tool (updated version of
HTSeq package). Since the updated version could generate different
results with the same input, Galaxy keeps the old version around for
reproducibility
For one of my tool wrappers (htseq-count) in the toolshed, I point to an
image file in the Help section. At the moment, I'm including the image
in the repository as static/imagescount_modes.png and pointing to it in
the wrapper.xml file with .. image:: /static/images/count_modes.png.
Hi Lance,
I answered this in your previous email - here's the answer:
To make this work in the tool shed, make the static directory that contains the
image file a relative path in the tool config. For example, your repository
has the following structure:
htseq_count
htseq-count.xml
Thanks for the quick response Greg. I tried this and uploaded an update
to the testtoolshed and installed that in a test instance of Galaxy.
Unfortunately, it didn't seem to resolve the issue. Galaxy still
renders the html with the image source pointing to the same location
(e.g.
Hello Lance,
Sorry this didn't work. I've opened the following Trello card for this issue.
https://trello.com/card/toolshed-handle-images-defined-in-help-sections-of-tool-configs-contained-in-a-repository/506338ce32ae458f6d15e4b3/725
Thanks,
Greg Von Kuster
On Mar 22, 2013, at 1:50 PM,
Hello,
I have a question for the many galaxy admins here. I am in the process
of setting up a local galaxy install submitting the jobs as real users
to our local SGE cluster. I am trying to figure out the best way to load
large datasets (Sequence files etc..) stored in the local clusters
Nate Coraor wrote:
On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote:
I have been running a Galaxy server for our sequencing researchers for a while
now and it's become increasingly successful. The biggest resource challenge for
us has been, and continues to be disk space. As such, I'd like
Hi,
We're running a private Cloudman Galaxy on AWS for small-scale proteomics
work. Lately the whole History of the main user id we use has occasionally
disappeared, ie. on login the History is empty. The datasets aren't hiding
in Deleted Datasets. They appear to still be there
in
Jens,
This isn't possible right now but has been suggested in the past. I've created
a Trello card for the idea that you can comment/vote on:
https://trello.com/c/zQcLM6I4
Best,
J.
On Mar 22, 2013, at 6:04 AM, Keilwagen, Jens wrote:
Hi guys,
I'm wondering whether it is possible to have
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