I'm running the latest stable.
The 500 error seems to be coming from the toolshed. Do you also get a 500 error
at the toolshed URL in my previous message?
There is nothing other than standard info line from the request in my pasted
log. I'm not able to get to the log right now, but I'll send i
Hi Lance,
What version of Galaxy are you running? Is the 500 error coming from your
Galaxy server or the tool shed server? Can you send the relevant information
from your Galaxy paster log when attempting to reinstall?
Thanks,
Greg Von Kuster
On Jun 11, 2013, at 3:52 PM, Lance Parsons wro
>> Trackster displays an error after opening a saved view:
>>
>> ***
>> Error: The requested genome file
>> (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be
>> opened. Exiting!
>> sort: write failed: standard output: Broken pipe
>> sort: write error
> [galaxy@q ~]$ /bin/cuffdiff
> /bin/cuffdiff: /usr/lib64/libz.so.1: no version information available
> (required by /bin/cuffdiff)
> cuffdiff v2.0.2 (3522)
This definitely indicates a problem with your cuffdiff install. Did
you build cuffdiff on that system or install in some other way? (very
odd
Hello,
When we run cuffdiff from the command line we get this;
[galaxy@q ~]$ /bin/cuffdiff
/bin/cuffdiff: /usr/lib64/libz.so.1: no version information available
(required by /bin/cuffdiff)
cuffdiff v2.0.2 (3522)
It looks like we are using a more recent version of cuffdiff than is
supported by th
Hello all!
I've recently started using Galaxy, and it's a fantastic piece of
software. However, I had a question about a possible feature, and any
suggestions on how to implement it.
My use case involves working with a lot of histories, and I need to
jump back and forth between them fairly freque
Hello,
I am trying to understand how the upload.py file works. I have already spent a
long time trying to figure this out, but I just cannot at all understand where,
for example, a pasted text input is saved. Let's say, for example, I wanted to
make any pasted text input all caps. Where would I
I have run into an issue when trying to reinstall a tool that was
originally installed via migration scripts (toolshed version of picard).
When I attempt to reinstall (after successfully uninstalling) I get a
500 error. After a bit of poking around, it seems that this URL
generates the 500 er
Thank you Jeremy.
The new wiki page looks great!
Regards,
Linda
From: Jeremy Goecks
To: Linda Cham/Poughkeepsie/IBM@IBMUS
Cc:
Date: 06/11/2013 12:56 PM
Subject:Re: [galaxy-dev] Trackster set display mode - Output looks all
the same
Hi Linda,
1- Sho
Hello all!
I've recently started using Galaxy, and it's a fantastic piece of
software. However, I had a question about a possible feature, and any
suggestions on how to implement it.
My use case involves working with a lot of histories, and I need to
jump back and forth between them fairly freque
Anna,
Try following these steps:
(1) Make your history accessible (Share or Publish --> Make History Accessible
by Link).
(2) Export your history again; make sure to wait until you can use the URL to
download a .gz file of your history.
(3) Try importing it via URL to the Huttenhower Lab Galaxy
Hi Linda,
1- Should the "Set display mode" give out different output?Not yet. VCF visualization is new to Galaxy, and mode switching isn't implemented yet. (It will be implemented in the next release.) What you're seeing is the display of individual variants; of course, trying to view so many varia
Even though the dialect name changed, the existing database urls should be
compatible (postgres:///...). Did you find this not to be the case?
-Dannon
On Mon, Jun 10, 2013 at 12:54 PM, Richard Burhans wrote:
> The SQLAlchemy "postgres" dialect was renamed to "postgresql". Changing:
>
>
Hi,
Our lab recently installed a local version of Galaxy on Mac OS X 10.8
and can access it at localhost:8080. Now we are trying to install
Bowtie version 1 but need help getting it to work. At this point we do
not see the tool listed on the left side of the Galaxy menu. Here are
the exact steps w
The SQLAlchemy "postgres" dialect was renamed to "postgresql".
Changing:
database_connection = postgres:///...
to:
database_connection = postgresql:///
in the ini file causes Galaxy (tool_shed in my case) to fail to start
as the "postgres" dialect is mentioned by name a fe
This message should be associated with a particular step in the
workflow. If you can tell us what tool it is that will help to
diagnose. The message means that a parameter that could not be checked
until the workflow ran had an invalid value.
--
James Taylor, Assistant Professor, Biology/CS, Emory
Hi,
I also have that error in the latest toolshed:
AssertionError: Attempting to set field 'topology' to value '['-c']' in
form 'tool_form' threw exception: multiple matches to value/label "c" in
list control control: If the above
control is a DataToolparameter whose data type class does not inc
Hi.
I have uploaded fasta files on the main galaxy server through my FileZilla
program. In want to transfer them to the Galaxy at the Huttenhower Lab (see
http://huttenhower.org/galaxy/root) page and to do that go to history list
when I am logged in at both locations and I select 'Import a Hi
I just have symlinked the files to the right location. Is this the
correct solution?
Further, I had to remove the 'chr' in the chrom len files to make it work.
Cheers,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 06/11/2013 03:26 PM, Joachim Jaco
Dear all,
I updated to the latest Galaxy stable code, and updated the
datatypes_conf.xml.
Trackster displays an error after opening a saved view:
***
Error: The requested genome file
(/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not
be opened. Exi
Hello,
Thanks all, but it it turns out my problem was that the line saying to use the
0.0.0.0 host was commented out.. That was stupid..
Thank you,
Daniel
On Jun 11, 2013, at 6:46 AM, Quang Trinh wrote:
> Hi Dan and Joachim
> You can also try what my students put together, which is based on
Thanks Dannon.
I am going with postgres for now while mysql is being fixed.
Regards,
Linda
From: Dannon Baker
To: Linda Cham/Poughkeepsie/IBM@IBMUS
Cc: Björn Grüning ,
Galaxy Dev
Date: 06/06/2013 04:41 PM
Subject:Re: [galaxy-dev] Installation of 20130603 Gala
Hi Simon,
I just installe dour fasta_stats repository form the test tool shed and
successfully executed your fast statistics tool, so I am not able to reproduce
this behavior. There must be a configuration problem in your local Galaxy
instance that is resulting in this behavior, but I cannot t
Hi.
Running standalone Galaxy stable_2013.06.03 version on RH6.2 with postgresl
db with GPFS filesystem.
Setup via the directions in
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
to run all jobs through the LSF DRMAA runner.
job_conf.xml:
Hi,
is every test shown, also if it runs successfully?
I'm just wondering because there is no installation test shown. And the
diff (is it truncated after X lines?) looks like the entire output is
missing.
Ciao,
Björn
> On Tue, Jun 11, 2013 at 9:18 AM, Björn Grüning
> wrote:
> > Hi,
> >
> > my
Hi Peter,
Indeed a caching issue.
Any chance we can improve that output? The diff is not really helpful.
Thannks,
Björn
> On Tue, Jun 11, 2013 at 9:18 AM, Björn Grüning
> wrote:
> > Hi,
> >
> > my augustus repository is shown under the summary page "Latest
> revision:
> > failing tool tests"
On Tue, Jun 11, 2013 at 9:18 AM, Björn Grüning <
bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
> Hi,
>
> my augustus repository is shown under the summary page "Latest revision:
> failing tool tests" but I could not see any failing test in the
> repository.
>
> http://testtoolshed.g2.bx.psu.edu
Hi,
my augustus repository is shown under the summary page "Latest revision:
failing tool tests" but I could not see any failing test in the
repository.
http://testtoolshed.g2.bx.psu.edu/view/bgruening/augustus
Cheers,
Björn
___
Please kee
Hello Linda,
Thanks for your suggestions.
i removed the line from xml file but now i am getting different error.
# ERROR
--
# ERROR A USER ERROR has occurred (version 2.5-2-gf57256b):
# ERROR The
Hi Daniel,
Make also sure you use correct firewall settings ('security groups') in
EC2. They are described the Galaxy wiki
(http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted?highlight=%28security%29|%28group%29),
but there are some small differences with the setting applied by
CloudLa
30 matches
Mail list logo
