Hi Nate,
We have found the solution to our/this issue. The way we have our
Galaxy instance configured is to have users required to log on. So in the
universe.wsgi.webapp.ini file we had set the User and Security settings to:
# Force everyone to log in (disable anonymous access).
#require_lo
Edward Kirton wrote:
> hi, we are getting the following error migrating from 79 to 80.
> curiously, my own galaxy didn't have this problem, but another
> developer here was getting this error. i moved him from sqlite to
> postgres but that didn't help.
> thanks for any assistance,
> ed
Hi Ed,
Is
Minor correction. It wasn't commented out...
# Force everyone to log in (disable anonymous access).
require_login = True
But yes, changing to
Require_login = False
Fixed the problem.
Thanks Iry.
Dave
On 9/1/11 8:42 AM, "Iry Witham" wrote:
> Hi Nate,
>
> We have found the solution to
This is similar to something we've done for workflows in our instance of
Galaxy. Dannon actually suggested I push a copy of my changes out so he can
review them and potentially add them to galaxy central. I've been
delinquent in doing this push. It's not exactly what you are talking about
but si
Galaxy is currently using vcfPytools for vcf support in a few tools as
well as for viewing in Trackster. Unfortunately, vcfPytools does not
support the latest version of vcf (4.1) and thus is causing issues when
used with the output of many newer variant callers such as Freebayes.
I contacted
Hi,
On our Ubuntu install stat packages and all that require rpy work fine.
On our CentOs install seeing this stubborn error that I did see from previous
post to be difficult to fix.
At first suspected the SGE issue - environment not transferring to compute
nodes. After changing the app to ru
i've been developing within Galaxy for awhile now and have been enjoying it
quite a bit. i've seen portions of similar ideas in the past, but never
cohesively assembled and so well realized.
i'd like to make some suggestions for further code collaboration / community
contributions.
my default
Hi Petr,
I am going to forward your email to the galaxy-dev list so that the
development community can offer comments/suggestions.
Best,
Jen
Galaxy team
On 8/30/11 2:27 AM, Petr Novak wrote:
Hi everybody,
I am developing the application on Galaxy server. One of the requirement
is to create
why not create a simple "export" tool? perhaps with the option to cp
or symlink.
On Thu, Aug 4, 2011 at 9:57 PM, colin molter wrote:
> Hi all,
> i am still stuck with the same problem.
> Is there a way to directly move/copy data from your galaxy history to a
> given location in the filesystem of
additional info:
it is possible on the same node to run manually
./gsummary.py
with the header:
#!/usr/bin/env python
import sys, re, tempfile
from rpy_options import set_options
set_options(RHOME='/apps1/R/2.13.1/intel/lib64/R')
from rpy import *
Where else can there be an env setting to pre
Read QC intermediate files account for most of the storage used on our
galaxy site. And it's a real problem that I must solve soon.
My first attempt at taming the beast was to try to create a single read QC
tool that did such things as convert qual encoding, qual-end trimming, etc.
(very basic fun
FWIW: This sounds like a useful idea to me.
My users are struggling with output names currently being generated by
complex workflows where many tools do something like
label="${tool.name} on ${on_string}: reordered ${outputFormat}" - that
might be ok for a single step but after traveling through a
This is a big part of the reason we did this.
I will push it out for the galaxy team to look at. If for some reason the
don't approve it I can share our change directly with you.
Dave
On Sep 1, 2011, at 6:39 PM, "Ross" wrote:
> FWIW: This sounds like a useful idea to me.
>
> My users are st
Hello,
I am working on a local install of Galaxy and when running a test data set I
get this error when invoking the Fastqc commans:
/home/mnkyboy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 20
class FastQC():
^
SyntaxError: invalid syntax
This is Illumina data from a single tile of qseq.txt
Hi all,
So I am writing XML files for an analysis pipeline. The first step in the
pipeline is to index the reference, the resulting files of which I have put
into the files_path directory that I get from using $output.files_path. But
then I want to be able to get access to that path in a subsequ
Hi Mathew,
The tool xml has a clunky way of finding the fastqc perl script -
which has to be in the same directory as the jars it requires:
rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file
-n "$out_prefix" -f $input_file.ext -e
${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/f
Nikhil,
You've found an old wart - try using extra_files_path
I don't remember exactly why but it's write to files_path but read
from extra_files_path
:0
On Fri, Sep 2, 2011 at 9:21 AM, Nikhil Joshi wrote:
> Hi all,
>
> So I am writing XML files for an analysis pipeline. The first step in the
>
On Thu, Sep 1, 2011 at 9:00 PM, Trevor Wennblom wrote:
> ...
> given that python has syntactically significant whitespace, i also
> try to maintain the convention of indentation with four-spaces.
> i've noticed this isn't consistent within the codebase, but does
> seem to be the preferred style s
On Thu, Sep 1, 2011 at 11:02 PM, Edward Kirton wrote:
> Read QC intermediate files account for most of the storage used on our
> galaxy site. And it's a real problem that I must solve soon.
> My first attempt at taming the beast was to try to create a single read QC
> tool that did such things as
On Thu, Aug 4, 2011 at 9:57 PM, colin molter wrote:
> Is there a way to directly move/copy data from your galaxy history to a
> given location in the filesystem of the same galaxy server?
2011/9/1 Edward Kirton
> why not create a simple "export" tool? perhaps with the option to cp
> or symlink
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