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 this
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 iry.wit...@jax.org wrote:
Hi Nate,
We have found
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
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 colin.mol...@gmail.com 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
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
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 ross.laza...@gmail.com wrote:
FWIW: This sounds like a useful idea to me.
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
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:
command interpreter=python
rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file
-n $out_prefix -f $input_file.ext -e
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 najo...@ucdavis.edu wrote:
Hi all,
So I am writing XML files for an analysis pipeline. The
On Thu, Sep 1, 2011 at 9:00 PM, Trevor Wennblom tre...@well.com 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
On Thu, Sep 1, 2011 at 11:02 PM, Edward Kirton eskir...@lbl.gov 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
14 matches
Mail list logo
