Hi Simon,
you are right. Public usernames, or usernames associated with a
repository can't be changed. If you can that is a bug, please fill a
trello card with it. The reason is to guarantee reproducibility. If
anyone has installed your repository the triple
(username,revision,toolshed) is saved
Hello Galaxy folks
I'm building a tool to run the Trimmomatic program, and I've encountered
an issue with filtering options from an external .loc file based on the
value of a parameter which is defined within a conditional block.
The parameter definition looks like this:
...
conditional
Hello Simin,
Bjoern is correct - if this is possible (which it looks like it is from your
traceback), then a bug has been introduced somewhat recently. We'll take a
look at this today and get a fix committed. Thanks for reporting this.
Greg Von Kuster
On Sep 4, 2013, at 3:17 AM, Bjoern
Hi all
I installed bismark from the toolshed (bgruening) with all dependencies
having been installed successfully and I generated the genomes according to
the instructions.
While trying to test the tool I got the following error.
galaxy.jobs.handler ERROR 2013-09-04 13:14:26,267 Failed to
Hi Nikos,
Hi all
I installed bismark from the toolshed (bgruening) with all
dependencies having been installed successfully and I generated the
genomes according to the instructions.
While trying to test the tool I got the following error.
galaxy.jobs.handler ERROR 2013-09-04
Simon,
I am unable to reproduce this behavior on my local tool shed
installation, which revision are you running?
--Dave B.
On 09/04/2013 06:57 AM, Greg Von Kuster wrote:
Hello Simin,
Bjoern is correct - if this is possible (which it looks like it is from your
traceback), then a bug
Hi Bjørn
that does not look like a bismark error. Is it happen with other tools
as well?
No, I have only experienced it with Bismark.
Not sure, sorry. But you should migrate to the new job configuration,
better sooner than later.
I am starting to get that idea. There are jobs still running
Adam,
Thanks for the report, I've updated that wiki page.
--Dave B.
On 09/04/2013 01:55 PM, Adam Brenner wrote:
http://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets
There are 5 scripts included in the Galaxy distribution that
can be used to clean up
http://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets
There are 5 scripts included in the Galaxy distribution that
can be used to clean up unwanted histories, libraries and
datasets. There are located in the
nwwl(GALAXY_ROOT)/scripts/cleanup_datasets
Hi Dave, Greg,
Thanks for your reply.
I'm running a recently checked out stable branch. hg log shows this tip:
changeset: 10473:c42567f43aa7
tag: tip
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
On Sep 4, 2013, at 10:08 AM, Nikos Sidiropoulos wrote:
Hi Nate
Yes, it is a multiprocess setup. But is it because we have more than one
web-servers, handlers or both?
Because if it's just the web-servers I could just scale it down to one since
it doesn't seem necessary with our number
Hello,
To use Velvet, a local, cloud, or slipstream Galaxy is needed. Then the
tool can be installed from the Tool Shed and used. The screencasts
Introduction to Galaxy ToolShed 1/2/3 walk through the general process
when using CloudMan Galaxy:
http://vimeo.com/user20484153
On Sep 4, 2013, at 9:17 AM, Nikos Sidiropoulos wrote:
Hi Bjørn
that does not look like a bismark error. Is it happen with other tools
as well?
No, I have only experienced it with Bismark.
Not sure, sorry. But you should migrate to the new job configuration,
better sooner than
Hi Nate
Yes, it is a multiprocess setup. But is it because we have more than one
web-servers, handlers or both?
Because if it's just the web-servers I could just scale it down to one
since it doesn't seem necessary with our number of users. It's would be
nice not to have to restart even for the
Hello Devs,
I've been trying for a while now to get ProFTPD working for our local
instance. I have:
1) Modified pg_hba.conf
2) Set up the ProFTPD config files
3) Disabled PBKDF2 password encryption by adding use_pbkdf2 = false to
universe_wsgi.ini
I've read through the posts from others with
Hi Alistair,
I have seen error output like this from mercurial when the client is running a
newer version than the server.
Maybe you recently upgraded your machine, and your mercurial version is now too
recent.
Hope that helps. Of course, it may be a complete red herring, YMMV. ;-)
cheers,
Hi everyone,
I want to use the hg_g1k_v37.fa on my local Galaxy,but I can not find this
data.When I use the command :
rsync -avzP
rsync://datacache.g2.bx.psu.edu/indexes/hg_g1k_v37/seq/hg_g1k_v37.fa
the error occurred:
receiving incremental file list
rsync: link_stat
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