Thanks Ross! Unfortunately I still have the same error. Although I can
directly run galaxy via the command run.sh, the system service fails with
the error I showed before. In other words this works as the galaxy user:
./run.sh --restart
This does not work when I run it as root (or when root
Dear galaxy developers,
When I use the EMBOSS tool:
trimesthttps://main.g2.bx.psu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS%3A%20trimest102/5.0.0,
Trim poly-A tails off EST sequences , within galaxy
The sequences names in the fasta output file comes out without
Is bowtie2 available on galaxy cloudman? If not, when will it be available?
Thanks,
Theresa Murphy
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Hi guys,
I was searching for a possiblity to dynamically load and run R scripts and I
found
http://dev.list.galaxyproject.org/dynamic-loading-of-tools-tt4138600.html
I know that it might be a security issue, but we only have a local instance
here.
Optimally an R script can be loaded into the
I figured it out after some more digging. The /etc/init.d script had a
Python flag -S which narrows down the paths where Python will search for
modules. The path with pyaml was excluded and could not be found. So, I
removed the -S flag.
And then, I almost forgot to run the command to make it
Yes, this is good suggestion. The good news is that the functionality is
already implemented in the soon-to-be-released version of CloudMan.
On Fri, Jun 14, 2013 at 6:52 PM, Ravpreet Setia
ravpreet.se...@oicr.on.cawrote:
Initially only one volume is shown on Amazon's EC2 management console.
Hi Teresa,
It's not available on the curent release but we are finalizing a new
release that will make addition of tools very straightforward so, if not
included by default, it will be easy to do.
Thanks for using Galaxy.
On Sun, Jun 16, 2013 at 4:25 PM, Murphy, Theresa
It is quite tedious to do so if you have many instances running. Is there a way
to automate this step? Thanks.
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If you're starting a bunch of new clusters at once, I'd look into using the
Share-an-instance functionality to create a single base configuration
with the volume size you prefer. This would allow you to have a predefined
volume (with a specific size) that starts automatically. The share_string
Hi,
I starting getting this error since late galaxy update
I get data from UCSC Main (local), but when I click display at UCSC main
I get:
Not Found
The requested URL /cgi-bin-root/hgTracks was not found on this server.
Please help
Thanks
--R
Dear list,
Yesterday, I noticed that the user quota setting on our Galaxy had a
problem - the list of user email address is missing from the manage quota
page. So I thought to give a Galaxy codebase update a try after backing up
the Galaxy dir and the database.
Running hg head gives me:
==
Hi Jens, the toolfactory (install from the admin menu - it's in the main
toolshed) allows admin users to paste and run arbitrary R scripts.
Yes, there are serious security issues exposing unrestricted scripting! So
the toolfactory only works for admin users and should never be installed on
Hello. I have installed Galaxy and run it successfully. Now I am trying to
configure it to use DRMAA job runner. I created a job_conf.xml file as
explained in the Galaxy wiki:
?xml version=1.0?
job_conf
plugins
plugin id=sge type=runner
load=galaxy.jobs.runners.drmaa:DRMAAJobRunner
When loading a data source in an iframe, the galaxy js is doing some sort
of invalid probing of the frame, leading to this error:
Blocked a frame with origin http://pk:8080; from accessing a frame with
origin https://tcga1.kilokluster.ucsc.edu;.
pk:8080 is the galaxy frame. Here is the
The error ERROR: could not read block 326 in file base/257536/259291:
read only 0 of 8192 bytes line makes me wonder if your database may have
been corrupt prior to the upgrade/dump. Some brief googling suggests that
this could be hardware failure induced among other things. Can you check
the
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