We're using ldap authentication on our cluster, so our /etc/passwd files don't
have any user data and the credentials are returned by ldap. You will have to
adjust this to your situation. You can rsync /etc/passwd from elsewhere or
fiddle with PAM to work something out for your key-based setup.
On Dec 18, 2012, at 12:51 PM, greg wrote:
> Hi guys,
>
> When I make a change to welcome.html how do I get galaxy to start
> displaying the new version?
>
> Thanks,
>
> Greg
In my experience you have to restart all web server paster processes.
Cheers,
Alex
_
On Dec 18, 2012, at 12:05 PM, "Ganote, Carrie L" wrote:
> Hi all,
>
> Right now I have drmaa running with Torque. I have a virtual machine with
> Galaxy installed on it, a filesystem mounted on the virtual machine that
> holds the dataset info, and a cluster that runs big jobs and also has a
There's also a shortcut that avoids having to click through the menus every
time. You can use a reload URL. For instance, if you were working with a local
instance and developing the tool 'mytool'. You can open the following url, keep
that page open and reload it when necessary to update the mod
On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk
wrote:
> I see that this issue came up before by Oleksandr Moskalenko in October but
> was unresolved then.
> Is there a workaround now?
>
> regards, Andreas
The velvet wrapper is not going to be usable for real user jobs until so
On Nov 27, 2012, at 9:37 AM, Peter Cock wrote:
> On Tue, Nov 27, 2012 at 2:20 PM, Oleksandr Moskalenko
> wrote:
>>
>> The "Right Way (TM)" I believe would be to have a universal resource request
>> selector that could be plugged into any wrapper simply by i
On Nov 27, 2012, at 6:06 AM, Andreas Kuntzagk
wrote:
> Hi Peter,
>
> thanks for your replies.
>
> On 27.11.2012 11:44, Peter Cock wrote:
>> On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk
>> wrote:
>>> Dear Peter,
>>>
As the author of several tool wrappers, I've been asking for a Gal
This is a pre-migration bwa. I've not updated this Galaxy instance, yet.
Here is a paste of used all options:
Will you select a reference genome from your history or use a built-in index?
history
Select a reference from history 3: StaphAureus_USA300_FPR3757 .fasta
Is this library mate-paired?
Hi,
I wonder if it's a known problem. I had a quick look through the mailing list,
but didn't see any relevant messages:
An extraction of a workflow from a history breaks on the bwa step:
Error - : invalid literal for int() with base 10:
'False'
URL: http://galaxy.hpc.ufl.edu/workflow/build_f
On Nov 5, 2012, at 2:15 PM, Carlos Borroto wrote:
> On Fri, Nov 2, 2012 at 6:03 PM, Oleksandr Moskalenko wrote:
>> Here is the blastn rule procedure code and the relevant snippet of the
>> default runner procedure. I just added the database based multiplier, so
>> this p
On Nov 2, 2012, at 3:58 PM, Carlos Borroto wrote:
>
> Please, could you share your rules related to blast. I would love to
> take a look at them.
>
> Thanks,
> Carlos
Here is the blastn rule procedure code and the relevant snippet of the default
runner procedure. I just added the database ba
On Nov 2, 2012, at 4:42 PM, Carlos Borroto wrote:
> On Fri, Nov 2, 2012 at 3:58 PM, Carlos Borroto
> wrote:
>> On Fri, Nov 2, 2012 at 9:53 AM, Oleksandr Moskalenko
>> wrote:
>>>
>>> The dynamic runner is alive and well thanks to the continuous work
On Nov 1, 2012, at 4:22 PM, Carlos Borroto wrote:
> Hi,
>
> I've been researching the possibility of using dynamic job runner in
> combination with job splitting for blast jobs. My main interest is to
> create a rule where both the size of the query and the database are
> taken into considerati
On Oct 29, 2012, at 3:20 PM, Todd Oakley wrote:
> Ann,
> Also to your request "I'd appreciate any input about MrBayes or a similar
> kind of tool."
>
> We are developing a suite of tools for phylogenetics in Galaxy. We are
> calling the tool suite Osiris.
>
> We are currently adding the
Hi Ann,
Configfiles is the way to go. I have writtent the BEAST (and TreeAnnotator),
Garli, and RAxML wrappers that are all available in the Galaxy ToolShed. BEAST
uses an input xml file that it can parse to execute the analysis. Garli can
take a config file that's generated by the Galaxy from
On Oct 18, 2012, at 12:28 PM, Christophe Antoniewski
wrote:
> Hi,
>
> Currently, the guide lines for using Apache as a reverse proxy to galaxy are
> to use the mod_rewrite module and the rewrite rules as explained in the
> galaxy wiki.
>
> I was wondering whether anybody has tried to use mo
Velveth wrapper passes the location of the database/files/xxx/dataset_yyy_files
to the velveth as an argument. Same paths are put into the output html file.
This method can't work anymore when jobs are submitted under real user names as
a real user doesn't have write permissions outside of the e
David,
For instances that run jobs under real user ids I think the job_name variable
in drmaa.py does not need the username component in this case anymore as the
batch system takes care of that and the resulting job name looks cleaner in the
qstat output. I use
@@ -184,10 +183,12 @@
Hi,
I am working on a wrapper that has multiple combinations of switches that lead
to the creation of the output files. For instance, one of the files can be
generated by conditions "A and B" and also by "A and C". FIrst, I tried the xml
and elements, but that didn't work. Next, I tried havin
On a related note, it's definitely nice to be able to consolidate the
configuration into a single universe_wsi.ini, but --daemon and --stop-daemon
are not sufficient for smooth operation of a multi web and job runner instance
of Galaxy. I wonder if anyone's already adapted run.sh to restart the
runner as a native DRMAA option. The only
remaining step is to populate the galaxy_user.username from our LDAP. All
modified galaxy code has been provided to the core Galaxy Team by the way.
Cheers,
Alex
On Aug 6, 2012, at 1:16 PM, Oleksandr Moskalenko wrote:
>
> On Aug 6, 2012, at 1
On Aug 6, 2012, at 1:01 PM, "Wood, James, D" wrote:
> I am a systems administrator for a cluster, and we use Torque and Moab as the
> resource manager and scheduler. I read that you can use drmaa to submit jobs
> as a different user other than the 'galaxy' user using the external scripts,
>
On May 23, 2012, at 11:42 PM, Ciara Ledero wrote:
> I didn't know that. Thanks for the reply! Now I have a new set of questions.
> First, how do I list myself as an admin? Should I just literally add my login
> detail in the config file? Second, my colleague would like to be able to edit
> and
I wonder if someone has a functional bowtie2 wrapper that they can share.
Thanks,
Alex
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Hi,
I have a problem with a tool wrapper I wrote handling input files with spaces
in their names. If a user uploads a dataset that has spaces in the file name,
e.g. "foo bar.xml" file then even though my tool, which uses the last "tmp
directory" method of handling multiple output files is prov
I needed to add a genome to the tracks in our local instance. However, the only
available genome is a multi-fasta file of about 1800 supercontigs. I preserve
the sanity of my clients I concatenated the fasta file and provided both
versions. The unfortunate part is that the contig annotation data
Hello,
I am getting consistent breakage for a C. Cerevisiae reference and mapped
dataset when trying to visualize the mapped data in Trackster. I'm running the
latest galaxy-dist and Trackster appears to be generally working since I added
a couple of reference genomes and users were able to vis
On Feb 8, 2012, at 10:07 AM, Jennifer Jackson wrote:
> Hello Alex,
>
> Both of these tools are in the Tool Shed. An easy way to locate these (and to
> search for tools/wrappers related to Galaxy in general) is:
> http://galaxy.psu.edu/search/getgalaxy/
>
> More about the Tool shed:
> http://wi
2-02-07 15:58:56,111 psycopg2 egg
> successfully loaded for postgres dialect
> galaxy.model.migrate.check INFO 2012-02-07 15:58:56,273 At database version 91
>
>
>
> On Feb 7, 2012, at 3:55 PM, Oleksandr Moskalenko wrote:
>
>> $ sh manage_db.sh -c ./dev_univer
ory.uninstalled column should exist as that column is
> created in the 0090 script. What was the log of your db migration upgrades
> that occurred when your database was migrated from version 85 to 90?
>
> Thanks,
>
> Greg
>
> On Feb 7, 2012, at 3:32 PM, Oleksandr Moskalenko w
I've upgraded my developmental Galaxy instance to the latest galaxy-dist
release with a transplanted the drmaa.py patch from galaxy-central. All .conf
files have been updated. However, I can't start the instance now The error
listed below is generated. I tried enabling/disabling the toolshed con
Scenario: Running two velvet jobs with the same parameters except for the
"Conditional (contig_lgth) either 0 or
1 (with minimum contig length = 500)
If the scheduler runs these jobs separately they produce expected results.
However, if they happen to start running simultaneously then one of
It seems that even under very light i.e. just a couple of long-running jobs
present load the job runner slowly, but steadily (1-3Mb per sec) grows its
memory consumption until it's killed by linux OOM killer.
My job runner config: http://pastebin.com/vMWDHAQm
I'm currently restarting the runner
On Nov 25, 2011, at 6:52 AM, Ivan Merelli wrote:
> Hi,
>
> I'm trying to use rgenetics in galaxy, but I have
> some problem in installting rpy-1.0.3 with R-2.13.1.
>
> I found this guide, which is about the same problem of mine:
> http://gmod.827538.n3.nabble.com/Rpy-1-0-3-and-R-2-13-1-td3359590
I have a diff for a bug that's been present in at least the last two releases
of galaxy-dist when python 2.6(.5) is used, which doesn't have SMTPError in
smtplib:
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -607,7 +607,7 @@ def send_mail( frm, to, subject, body, config
I would like to avoid reinventing the wheel if possible, so I wonder if anyone
has wrappers for Garli (https://www.nescent.org/wg_garli/Main_Page) and Tandem
Repeats Finder (http://tandem.bu.edu/trf/trf.html) they could share.
Thanks,
Alex
Got another problem with the bug reporting tool:
"POST /dataset/report_error HTTP/1.1" 500 -
"http://galaxy.hpc.ufl.edu/dataset/errors?id=775"; "Mozilla/5.0 (compatible;
MSIE 9.0; Windows NT 6.1; Trident/5.0)"Error - : local variable 'dataset_id' referenced before
assignmentURL: http://galaxy.h
Someone shared a history with me for the purpose of debugging their Galaxy
problem in our local Galaxy instance. I set the "error_email_to" to our bug
reporting email address, but I can't submit a bug report using the "bug" icon
in the history for datasets in an error state. The traceback is bel
ME.strip(), 'include'),
'src', '/usr/share/R/include', '/apps/R/2.13.1/include' ]
* Build rpy with
python setup.py install
On Sep 22, 2011, at 3:38 PM, Oleksandr Moskalenko wrote:
>
>
> On Sep 22, 2011, at 1:56
On Sep 22, 2011, at 1:56 PM, Assaf Gordon wrote:
> Hello,
>
> It seems this issue (rpy) pops up every now and then:
> Has anyone managed to get rpy-1.0.3 working properly with R-13.1 (including
> loading packages) ?
I already replied to Assaf, so this is a list copy. Yes, this combination
wo
Providing the correct environment using the .bashrc for the user that the pbs
jobs are submitted under works for me. Many thanks to Glen Beane!
Cheers,
Alex
On Sep 14, 2011, at 9:03 AM, Nate Coraor wrote:
> Glen Beane wrote:
>>
>>
>>
>>
>> On Sep
I need to get Galaxy to use tools that are not located in the system path. At
the command line I can export the PATH either manually or with environment
modules 'module load foo'. However, there doesn't seem to be a clear way to
pass the $PATH and other environmental variables to the pbs runner
Hello,
Considering the fact that a galaxy instance can grow to be quite large I wonder
what Galaxy backup strategies and implementations other people actually have in
use and are happy with.
Thanks,
Alex
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