Hi all,
I want to change the location of the toolshed database. First I copied
all contents to the new location, and next, I adjusted community_wsgi.ini:
file_path = /mnt/toolsheddb/community_files
However, the toolshed fails to start now, throwing this error:
RepoError: repository
/home/gala
Hello Joachim,
You may be the first that has tried this, so you're covering new territory.
You'll have to manually change the entries in the hgweb.config file located in
your Galaxy install directory. If your tool shed then starts up and you can
point your browser to it, you should reset the
Hello Hans-Rudolph,
If I remember correctly, the release in March did not properly handle the
scenario where new tool entries were made within an existing section of the
tool panel or new tool panel sections were added to specific locations of the
tool panel. In both these cases, the new entry
Thanks Greg, this works!
Joachim
@bitsatvib
On 08/27/2012 02:10 PM, Greg Von Kuster wrote:
Hello Joachim,
You may be the first that has tried this, so you're covering new territory. You'll have
to manually change the entries in the hgweb.config file located in your Galaxy install
directory
Hi Peter,
This feature has been on my list for some time. There was discussion about
this at the Galaxy Community Conference in July, and the priority for providing
this was raised at that time. However, my next chunk of work will be in the
area of enhancing the Galaxy framework to better han
On Aug 24, 2012, at 8:11 AM, Laure wrote:
> Hi galaxy users,
>
> I configured galaxy with external ldap authentification using apache proxy,
> so my galaxy users are automatically created in galaxy database.
> When I want to configure proftpd to work with galaxy as it is mentionned in
> galaxy
Hi Peter,
I assume you are using a Galaxy instance within your development environment
when developing new Galaxy tools so that you ultimately ensure your tool is
functionally correct. Adding a local tool shed to your development environment
will help you ensure that certain tool shed related
On Mon, Aug 27, 2012 at 1:58 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> I assume you are using a Galaxy instance within your development
> environment when developing new Galaxy tools so that you ultimately ensure
> your tool is functionally correct. Adding a local tool shed to your
> development
Hello,
I modified the Galaxy configuration file and would like to stop and re-start
the Galaxy process. Can you tell me how to do that?
Thank you.
___
Please keep all replies on the list by using "reply all"
in your mail client. To
Hello,
Can someone tell me if stopping and then restarting the Galaxy process would
prevent currently-running jobs from completing after the restart? Will all the
jobs remain in the queue after the restart? Also, what is the best way to
restart the Galaxy server? Users are complaining that j
On Fri, Aug 24, 2012 at 4:30 PM, Peter Cock wrote:
>> >>
>> >> Would anyone know about my question 1? If I install a local version
>> >> of Galaxy and connect it to our cluster, where is each user's
>> >> (uploaded?) data stored? How will the cluster jobs be able to access
>> >> the data?
>> >
>
Any ideas anyone?
Philip Mabon
Senior Bioinformatician
National Microbiology Laboratory
Public Health Agency of Canada
On Tue, Aug 21, 2012 at 10:34 AM, Philip Mabon wrote:
> I just upgrade our galaxy to the latest release : 7487:be81990d148a and
> ran the migration tool script for freebayes.
Hi Greg
Thank you very much for your e-mail
Unfortunately, we still see this behavior in
"changeset:7404:ec29ce8e27a1" (July 20, 2012 release).
All screen shots in my original e-mail (21-Aug) were made with a server
running the July release.
Regards, Hans-Rudolf
On 08/27/2012 02:18 PM, Gr
If you install the blast_datatypes repository into your Galaxy instance using
the tool shed installation process everything necessary is handled for you
automatically, but I understand you are not yet installing from the tool shed.
If you are not installing, you'll have to manually download th
Hi Phillip,
I'm not able to reproduce this behavior, so it's difficult to determine what
may be the cause. I have not seen others in the community encounter this
problem, but that may simply be due to the fact that no one is yet installing
the freebayes tool from the tool shed.
A possible wor
Hi Hans,
Sorry, I missed your information about your using the latest dist release in my
original response. See my inline comments.
On Aug 21, 2012, at 11:18 AM, Hans-Rudolf Hotz wrote:
> HI
>
>
> We have been struggling with this problem since we updated to
> "changeset:6799:40f1816d6857"
I responded to your original email, which I should have done initially. Sorry
for the back-and-forth on this.
On Aug 27, 2012, at 10:16 AM, Hans-Rudolf Hotz wrote:
> Hi Greg
>
> Thank you very much for your e-mail
>
> Unfortunately, we still see this behavior in
> "changeset:7404:ec29ce8e27a1
On Mon, Aug 27, 2012 at 3:31 PM, Greg Von Kuster wrote:
> If you install the blast_datatypes repository into your Galaxy instance
> using the tool shed installation process everything necessary is
> handled for you automatically, but I understand you are not yet
> installing from the tool shed.
E
On Mon, Aug 27, 2012 at 2:25 PM, greg wrote:
>>>
>>> How do users get data into Galaxy in your system?
>>>
>>
>> Mostly via the "upload" tool, or sometimes the remote
>> data tools (eg from UCSC). Some commonly used
>> files are also setup on our system as shared libraries
>> within Galaxy.
>
> It
Bonjour à tous,
Avec l'aide et le soutien de l'équipe Galaxy, nous venons de mettre en
ligne la liste de diffusion Galaxy France.
Cette liste a pour but de partager et communiquer sur nos différentes
expériences avec Galaxy au sein de l'hexagone.
La langue officielle de cette liste est le frança
I found that the problem happened if I used the UI for editing text. What I did
instead was edit the wiki using the text-based mode instead. If you have set
your
preferences to use the UI for editing by default, then you will need to change
it
back to use the text-based editing instead; I foun
Hello,
If I were to stop and re-start the Galaxy server with the run.sh script would
jobs that are aleady running or are in the queue be lost when the server is
re-started? If so, is there another method to use which would not lose the
running or queued jobs?
Thank you.
_
Unless something has recently changed, you will need to set up a cluster to get
jobs to persist across galaxy restarts.
You can do this with just a single node acting as both queue master and job
runner using sun grid engine (i think, I have not tried this myself)
Brad
On Aug 27, 2012, at 12:51
I already had that entry to the tool_data_table_conf.xml but still getting
the same error.
After some debugging and print statement, I found that it initially finds
the correct path to the 'sam_fa_indexes' when reading
tool_data_table_conf.xml in Galaxy installation directory but re-reads
another
If you refer to using one machine as master AND host simultaneously, which
you never tried: let me tell you it does work well with SGE/OGE. I have it
running, and it just works out great. It enhances the load control on that
machine, due to the great configuration possibilities on queue level (max.
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