On Mon, Mar 3, 2014 at 6:33 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Mar 3, 2014, at 1:13 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Guys,
Is this stuff on the wiki?
Not completely yet.
The only mention I found was something in passing on last
month's news page:
Hi Peter,
Hello all,
I've mentioned before that a forthcoming update to the BLAST+
Galaxy wrappers would be adding a most customisable output
option with pick-your-own columns. This is available to test now
from the Test Tool Shed, along with other enhancements like
more masking tools and an
On Tue, Mar 4, 2014 at 2:38 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
On Mar 4, 2014, at 5:19 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Mar 3, 2014 at 6:33 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Mar 3, 2014, at 1:13 PM, Peter Cock p.j.a.c...@googlemail.com
Hi Bjoern,
Thank you for your clarifications. I have tried installing bowtie2 using both
variations, once with both wrapper and dependencies and once with only wrapper
(since I have dependencies installed on the system). In either case even after
editing the .loc file I cannot see the indices
Hi Ravi,
can you attach the loc file, do you see anything in the Galaxy log files
about bowtie2, try grepping for bowtie2.
Cheers,
Bjoern
Am 04.03.2014 18:07, schrieb Ravi Alla:
Hi Bjoern,
Thank you for your clarifications. I have tried installing bowtie2 using both
variations, once with
Hi Bjoern,
Please find the bowtie2 and bowtie .loc files. In the paster.log file I see
these entries for bowtie
galaxy.tools.data DEBUG 2014-03-04 10:14:11,048 Loaded tool data table
'bowtie_indexes'
galaxy.tools.data DEBUG 2014-03-04 10:14:11,051 Loading another instance of
data table
Hi there,
I've run into an issue with the pbs runner involving pbs server name
strings becoming 'unicode' rather than 'str'. The pbs_python lib can't
pass unicode strings down to the C library, which results in this
failure:
https://gist.github.com/anonymous/9352218
The very top line of log
Hi,
can you check if the file tool_data_table_conf.xml contains an entry
about bowtie2_indexes ... or the table shed_data_table_conf.xml ... in
one of them should be one entry with bowtie2_indexes.
That warning should not be there I think:
galaxy.tools.parameters.dynamic_options WARNING
Hey Eric,
Odd - is MSI still using tool runner URLs in universe_wsgi.ini or have
you guys transitioned to job_conf.xml. If you are using a job_conf.xml
file - out of curiosity are you explicitly declaring an XML encoding
at the top of it? Not that this would be the wrong thing to do - I am
just
Hey John,
We're using job_conf.xml, which does not specify an encoding. It doesn't
seem to be the XML parsing at issue; if you omit the restarting of
galaxy step, jobs go through just fine. Only when galaxy is restarted
while the job is running (and destination_params must therefore be
reloaded)
Hello all
The call for abstracts for BOSC 2014 is out. See below for details.
If you have questions I'm sure that Peter, Brad, Chris, and Hans-Rudolf,
all frequent contributors to this list, would be answer them. And glad to
see that GigaScience, a GCC sponsor, is also sponsoring BOSC this
Hello,
I am trying to visualize a large genome (Large number of scaffolds) and
a large (bam file) in trackster on our local galaxy instance (running
release_2014.02.10).
When ever I try to do the above I see the following error in the logs:
File bbi_file.pyx, line 215, in
Has anyone had any success in getting cluster jobs running as the real user?
I've got our server happily working with LSF via drmaa but all jobs run as the
galaxy user and I would like to be able to separate out the jobs on a per user
basis. I've followed the instructions at
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