Hi All,
I am attempting to do a local install of Galaxy using the galaxy-dist source.
While testing some of the the tools I have run into a problem with the laj
Pairwise Alignment Viewer tool. I have also tested this on the test server
http://test.g2.bx.psu.edu/ and I am getting a very similar
Ok, now it's the other install that doesn't work anymore.
Looks like a cuckoo's nest, they must be sharing something they
shouldn't, first arrived first served.
But I really don't see what's going wrong:
- They run from distinct galaxy copies
- They use different databases
- They use different
Hi,
I have a tool that takes a zipped archive as input, finds all the
sequence files (~90 of them), separates them by barcode, does a little
extra processing and outputs a single fasta file. I would like this to
run on Galaxy in a workflow with a few other tools.
I know there have been d
Branden Timm wrote:
> Sorry to dig up this old thread, but how do you remove the check
> that prevents galaxy running on 2.7? One of my developers just
> updated his workstation to Ubuntu 11.04 (Py 2.7) which is preventing
> him from running Galaxy. I'm not sure whether it would be better to
> re
Sorry to dig up this old thread, but how do you remove the check that
prevents galaxy running on 2.7? One of my developers just updated his
workstation to Ubuntu 11.04 (Py 2.7) which is preventing him from
running Galaxy. I'm not sure whether it would be better to remove this
check or to just
When I use : default_cluster_job_runner = drmaa://-q longq -V/
I obtain this error :
/DeniedByDrmException: code 17: Multiple different queues - longq workq
- found. Job rejected./
workq is our default queue. It seems that it doesn't overwrite the queue
but if an user type : qsub -q longq...
Nikolai Vazov wrote:
>
> Hi, Nate,
>
> When trying to execute
>
> PYTHONPATH=/home/galaxy/galaxy-dist/scripts/scramble/lib python26
> setup.py egg_info --tag-build=_8.4.2_static bdist_egg
>
> I get
>
> Traceback (most recent call last):
> File "setup.py", line 52, in
> from scramble_lib
Hi, Nate,
When trying to execute
PYTHONPATH=/home/galaxy/galaxy-dist/scripts/scramble/lib python26
setup.py egg_info --tag-build=_8.4.2_static bdist_egg
I get
Traceback (most recent call last):
File "setup.py", line 52, in
from scramble_lib import *
File "/home/galaxy/galaxy-dist/s
Hello,
This is a bug and has been fixed. I reran your analyses on our test server and
they completed successfully, so you should be good to go.
Best,
J.
On May 3, 2011, at 6:08 AM, shamsher jagat wrote:
> Jeremy,
>
> I have been trying to follow the steps in filtering Cufflink out put files
On 05/03/2011 03:11 PM, Sylvain Thomas wrote:
> Hi
>
> I currently use a galaxy server with cluster. This cluster uses SGE.
> I'd like to specify a queue other than the default.
> I have tried many combinaisons with drmaa:/// without success. The queue
> used is always the default one.
Here is wh
Nikolai Vazov wrote:
>
> Hi again,
>
> The version of the PostgreSQL server I am trying to connect to is
> actually 8.3. The DB department say they will soon move to 9.0.
> The psycopg2 version in my eggs.ini for Galaxy is 8.4.2:
>
> psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg
>
>
Nikolai Vazov wrote:
>
> Hi, Nate,
>
> I am trying to follow the designed steps below.
>
> 1. I downloaded psycopg2 2.0.13. Does it matter where in galaxy-dist
> directory I place it?
>
> 2. I modified setup.py - OK
>
> 3. pg_config --version gives :
>
> PostgreSQL 8.1.23
>
> I don't really
Hello, and sorry for the late reply
All the answers are yes, since it didn't stop working at all.
I fear transferring the data again now...
Hans-Rudolf Hotz wrote:
well, do it the hard way and start from "square one":
- is galaxy working out of the box (fresh checkout, using SQLite)
- is g
Hi
I currently use a galaxy server with cluster. This cluster uses SGE.
I'd like to specify a queue other than the default.
I have tried many combinaisons with drmaa:/// without success. The queue
used is always the default one.
Does anyone has solved this problem?
Thanks,
Sylvain
--
Sylvai
Hi again,
The version of the PostgreSQL server I am trying to connect to is
actually 8.3. The DB department say they will soon move to 9.0.
The psycopg2 version in my eggs.ini for Galaxy is 8.4.2:
psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg
Do you think it will work?
3. Find t
Hi, Nate,
I am trying to follow the designed steps below.
1. I downloaded psycopg2 2.0.13. Does it matter where in galaxy-dist
directory I place it?
2. I modified setup.py - OK
3. pg_config --version gives :
PostgreSQL 8.1.23
I don't really get what you mean by
" make sure the version yo
Jeremy,
I have been trying to follow the steps in filtering Cufflink out put files
you have described in one of the previous messages (
http://gmod.827538.n3.nabble.com/Re-downstream-analysis-of-cuffdiff-out-put-td2836457.html
):
I have shared histroy with you, but in summary:
File 35: when F
Hi all,
In biology we often want to use italics, the key examples
that come to mind are species and gene names. I think
it is natural therefore to want to be able to use italics in
the description of data resources in Galaxy's loc files.
For example, in our local Galaxy for the BLAST databases
li
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