.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Mar 25, 2014, at 11:15 AM, Raj Ayyampalayam mailto:ra...@uga.edu>> wrote:
Jeremy,
I uploaded my dataset to the main galaxy site and the visualization
failed.
Here is the link to the history:
problem on both main and my local galaxy instances
(local is tracking latest galaxy-dist).
Thanks,
-Raj
On Wednesday, March 05, 2014 11:25:26 AM, Raj Ayyampalayam wrote:
I checked the version of bx-python egg and confirmed that it is
bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg.
I
You are probably missing the samtools and bowtie2 dependencies. Make
sure Galaxy can find the binaries.
-Raj
On Fri Mar 7 00:16:07 2014, Langhorst, Brad wrote:
I’m slowly wrapping my head around the new data manager stuff… but I
don’t think I quite have it yet.
I was able to download hg19 us
our public server, share the datasets with me and I'll take a look.
Thanks,
J.
--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University
On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam mailto:ra...@uga.edu>> wrote:
Hello,
I am trying to visual
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 bx.bbi.bbi_file.
ta.py",
line 483, in convert_dataset
-Raj
On Fri Aug 2 00:51:39 2013, Raj Ayyampalayam wrote:
Here is the first part of the error (Traceback):
galaxy.tools ERROR 2013-08-01 22:56:16,590 Exception caught while
attempting tool execution:
Traceback (most recent call last):
File
"/panfs/pst
galaxy-dist/lib/galaxy/tools/__init__.py",
line 2264, in execute
return self.tool_action.execute( self, trans, incoming=incoming,
set_output_hid=set_output_hid, history=history, **kwargs )
File
"/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__
Hello,
My local cluster based galaxy installation was running fine till this
evening. Later I decided to test some workflows and got an error with
massive stack trace.
I can't make any sense of this. Here is the last part of the error. The
stack trace is literally 1000's of lines. Can somebody
Hello,
I am trying to come up with a number for our local galaxy storage
requirements when we go live (This is an installation for research at
our university).
I checked out the survey that was done a while back for the
GalaxyAdmins. It seems that the bigger installations have allocated
abo
on is "library_type is None" and
"library_type is not None".
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Mar 28, 2013 at 6:35 AM, Peter Cock wrote:
On Thu, Mar 28, 2013 at 4:36 AM, Raj Ayyampalayam wrote:
Hello,
I am trying to get the trini
Hello,
I am trying to get the trinity wrapper to work on our local galaxy
installation using the latest trinity version.
The main issue is that the Trinity.pl call has --SS_lib_type None in the
script file. The data I am using is unstranded paired end reads and I am
selecting None in the too
Hello,
I have a question for the many galaxy admins here. I am in the process
of setting up a local galaxy install submitting the jobs as real users
to our local SGE cluster. I am trying to figure out the best way to load
large datasets (Sequence files etc..) stored in the local clusters
stor
Hi Nate,
I am trying to rsync the indexes and getting a rsync error.
$ rsync -avz rsync://datacache.g2.bx.psu.edu/indexes/phiX .
@ERROR: chroot failed
rsync error: error starting client-server protocol (code 5) at
main.c(1530) [receiver=3.0.6]
Should I change anything in my command?
Thanks,
Hi Guys,
Thanks for the quick response. I installed the latest blast datatypes
from the toolshed and that fixed the issue.
Peter, can you also fix the $outfile.extra_files_path to
$outfile.files_path on line 5 in the makedb wrapper xml file.
Thanks,
-Raj
On Wednesday, March 20, 2013 10:
Hello,
I am setting up a local galaxy installation and using our local SGE
cluster to run the jobs as real users.
One of the first few tools I tested was the ncbi makebkastdb tool. When
I try to run it the history for that particular job is immediately shown
as follows:
0: (unnamed dataset
Hello,
I am interested in this "local upload file" tool. Can you please send
the files to me as well.
Thanks.
-Raj
On 6/8/12 4:36 AM, Alban Lermine wrote:
Hi,
There is also another solution if you don't want let users being able
to create libraries.
We have implemented this solution in our
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