So Ihave finally determined the cause and found a resolution for the
snpEff/java problem. The issue was the fact that the vrsion of Java on
the Ubuntu linux VM from AWS is 1.6.x snpEff 4.0e requires version 1.7.0
or higher. This is fine, but you willneed to manually upgrade the java
version. To
So I have finally determined the cause and found a resolution. The issue
was the fact that the version of Java on the Ubuntu linux VM from AWS is
1.6.x. GATK2 requires version 1.7.0 or higher. This is fine, but you
will need to manually upgrade the java version. To do so you will need to
comple
This is a new one for me. What configuration are you using for both your
'database_connection', and the 'amqp_internal_connection' in your
universe_wsgi.ini?
On Fri, Jun 13, 2014 at 12:29 AM, xlwang wrote:
> Hello,
> when i run my galaxy instance type:
> $ sh run.sh
> I get some error like
Hello,
when i run my galaxy instance type:
$ sh run.sh
I get some error like this:
Traceback (most recent call last):
File "/export/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 38, in
app_factory
from galaxy.app import UniverseApplication
File "/export/galaxy-dist/lib/g
On Wed, Apr 16, 2014 at 12:16 PM, Dooley, Damion wrote:
> Thanks for your input, John. I see, so from what you say, anything installed
> via pip in the virtual environment then exists in the module/class include
> namespace within galaxy python command line tool code. Good to know.
>
> I'll no
Thanks for your input, John. I see, so from what you say, anything installed
via pip in the virtual environment then exists in the module/class include
namespace within galaxy python command line tool code. Good to know.
I'll note that this approach is compatible with toolshed tools (I'm testi
Hi folks,
Has someone seen this behaviour? I'm trying to do a once-over maintenance
cleanup of our galaxy installs. The galaxy account is getting emailed nightly
with an error which is happening when it gets to delete_datasets.sh cron task,
basically:
AttributeError: 'NoneType' object ha
Ilya,
I fixed the igvtools_tile.xml tool config and pushed it to the toolshed.
Thanks for finding and reporting the problem.
JJ
On 11/27/12 3:18 PM, Sytchev, Ilya wrote:
Here's a link to one of the WIG files I am using:
https://www.dropbox.com/s/rv201lawduflr7j/Galaxy12-scc.wig.zip
I'd appreciat
Here's a link to one of the WIG files I am using:
https://www.dropbox.com/s/rv201lawduflr7j/Galaxy12-scc.wig.zip
I'd appreciate any pointers.
Thanks,
Ilya
On 11/27/12 3:57 PM, "Jim Johnson" wrote:
>
>
>
>Ilya,
>
>Could you send me a failing input file, and I'll try to find out what is
>failing
Ilya,
Could you send me a failing input file, and I'll try to find out what is
failing?
Thanks,
JJ
--
Message: 6
Date: Tue, 27 Nov 2012 07:22:30 +
From: "Sytchev, Ilya"
To: "galaxy-dev@lists.bx.psu.edu"
Subject: [galaxy-dev] No output from IGVtools tile
M
Galaxy assumes that tools that write to stderr indicate failure. There's
apparently some way
to set up regexps to get around that, but I don't know where to do that
(or if indeed that would work).
Command-line debugging works some, except when the web server's
environment (path, etc.)
differs
Here is a copy of the whole VirtualHost section.
Thanks,
Adhemar
ServerName lbas046.cnptia.embrapa.br
ErrorLog logs/galaxy_ssl_error_log
TransferLog logs/galaxy_ssl_access_log
LogLevel warn
SSLEngine on
SSLCertificateFile /etc/pki/tls/certs/lbas046.cnptia.embrapa.br.crt
SSLCertificateKeyFile
Hi Daniel,
I did use -e previously. The ?e was a typo in my post. I ran it again
and it tries, but fails to generate the file(s) as shown:
:galaxy@jaxgalaxydev01:/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist>
LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
fetch_on
ile (sshashi)
--
Message: 1
Date: Sat, 7 Jul 2012 14:10:45 -0500
From: "Dorset, Daniel C"
To: Iry Witham
Cc: "galaxy-dev@lists.bx.psu.edu"
Subject: Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10
Messag
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
On Behalf Of galaxy-dev-requ...@lists.bx.psu.edu
[galaxy-dev-requ...@lists.bx.psu.edu]
Sent: Saturday, July 07, 2012 11:00 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: galaxy-d
I would also like to voice my support for this feature. I wrote a wrapper
for bowtie that converts the SAM output to BAM after bowtie is finished just
to avoid the hassle of letting galaxy "know" that the SAM file existed
(didn't want to run Tophat).
After thinking about how I would go about deleti
> The general config file allows us to set a fixed project:
>
> default_cluster_job_runner = drmaa://-A a2010002 -p core
>
> And even set per-tool job settings. But we would like each user to have
> the ability to change those settings.
>
>
> What is the least intrusive way to set per-user nativ
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