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 t
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:
...
trueval
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 Gruen
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 genera
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 20
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 has
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 runn
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 un
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
> <<>>/scripts/cleanup_datasets
> directory and
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
reposit
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 n
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
http://wiki.gal
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 soo
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 t
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 this
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 "/hg_g1k_v37/seq/hg_g1k_v37
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