Hi,
I updated my galaxy distribution with
hg pull -u
Then tried to re-run galaxy and got an error:
$ ./run.sh
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File /home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line
1049,
On Tue, May 7, 2013 at 10:16 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Tue, Apr 30, 2013 at 2:04 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Dan,
Sure, you can configure per-tool job runners. This wiki page
(http://wiki.galaxyproject.org/Admin/Config/Jobs) should get you started
?
Thanks,
Dan
On Tue, Apr 30, 2013 at 4:47 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi,
I have some tools that run really quickly without using any kind of
cluster.
I would prefer not to run these tools on a cluster, as the overhead of
submitting these jobs makes them take much longer
Hi,
I have some tools that run really quickly without using any kind of cluster.
I would prefer not to run these tools on a cluster, as the overhead of
submitting these jobs makes them take much longer than they otherwise
would.
I have other tools that are computationally intensive and need to be
On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto
carlos.borr...@gmail.com wrote:
On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Re: login: I believe there's a redirect in place that moves you past the
older 'Return to the homepage' message automatically - I think you're
On Fri, Feb 1, 2013 at 8:41 AM, Stephen Groenewold
sgroenew...@idtdna.com wrote:
We’ve installed a local instance of Galaxy and are having trouble with the
first step of uploading files. The only thing that will currently upload is
text pasted into the URL/Text box.
Any attempt to upload a
; it records the lack of a current history which is
normal when you access those pages but haven't logged in yet)
On Tue, Jan 29, 2013 at 12:49 PM, Dan Tenenbaum dtene...@fhcrc.org
wrote:
Hi Carl,
On Tue, Jan 29, 2013 at 9:30 AM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Those are both
-
http://localhost:8080/history; Mozilla/5.0 (Macintosh; Intel Mac OS
X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56
Safari/537.17
And the last line repeats every 4 seconds (with timestamp updated).
Dan
C
On Wed, Jan 30, 2013 at 2:13 PM, Dan Tenenbaum dtene...@fhcrc.org
help.
Can you post the size, type, and name of the file you're trying to upload?
I can reproduce this by just typing hello, world into the
URL/Text: box on the Upload File page. Any file of any type seems
to trigger this problem.
Thanks,
Dan
On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum
the one
in Galaxy's eggs)?
I don't think so. I never knowingly installed it and in a fresh python
session, 'import sqlalchemy' returns an error that there is no such
module.
Thanks,
Dan
On Mon, Jan 28, 2013 at 4:50 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Mon, Jan 28, 2013 at 1:40
Hi,
I installed galaxy completely from scratch:
rm -rf galaxy-dist hg clone https://bitbucket.org/galaxy/galaxy-dist/
I'm not a mercurial expert but I think I have changeset
8530:a4113cc1cb5e; at least that's the first entry in hg log.
Then started galaxy like this:
cd galaxy-dist
./run.sh
luck!
It works! I changed the mime type to application/x-gzip, since
serialized R objects are gzipped.
Thanks,
Dan
On Thu, Jan 24, 2013 at 10:41 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi,
I have a tool wrapper with a param of type=data.
Currently, this renders as a text box
:58 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Wed, Jan 23, 2013 at 3:51 PM, Ross ross.laza...@gmail.com wrote:
Hi, Dan.
Using format=rda will restrict the list to history items of the 'rda'
datatype - but ONLY if the rda datatype has been defined!
The easiest way to do
Hi,
I'm trying to test out the functional testing mechanism by running it
on an existing Galaxy tool.
First I ran
./run_functional_tests.sh -list
which produced a list of tools I can test. I chose 'vcf_annotate' and
tested it as follows:
./run_functional_tests.sh -id vcf_annotate
This
Hi,
If I have a tool wrapper with this:
param name=x type=integer help=the x param/
I get an error when I start Galaxy:
galaxy.tools ERROR 2012-09-19 12:09:08,056 Error reading tool from
path: RGalaxy_test_tool/foo.xml
Traceback (most recent call last):
File
I'd like to have a tool that does not actually return anything (is
that possible?) but writes a file to the directory where Galaxy stores
uploaded data files, and tells Galaxy about it (perhaps that involves
writing to a database?). My tool is written in R.
Here is my scenario:
I want the user to
datatype). Then the user can just pass it to the
downstream tools just by specifying one parameter.
-- jt
On Tue, Sep 18, 2012 at 3:00 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
I want the user to upload a text file, then pass that text file, along
with several parameters, (in something we'll
Hi,
I notice that a param with type select renders differently
depending on how many options there
are. If there are 20 options, it appears as a normal select box. If
there are = 20 options, it looks like a text box (but it has
autocompletion and does have a dropdown menu), and Inspect Element
So, sounds like maybe this feature does not existI'd like to
request it (given a dataset, I'd like to be able to show the column
headers of that dataset in a select box).
Thanks,
Dan
On Wed, Aug 29, 2012 at 11:09 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi,
I have some code that makes
On Tue, Sep 4, 2012 at 4:57 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Sep 4, 2012 at 4:54 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
So, sounds like maybe this feature does not existI'd like to
request it (given a dataset, I'd like to be able to show the column
headers
Hi,
I have some code that makes a plot and creates a legend from a given
column name in the user's input data, which may have arbitrary column
names.
I'd like to create a dropdown list that has all the column names in
it, but I don't know the names beforehand; I won't know them until the
user
Hello,
Is there a way to do one or both of the following:
1) Group a set of related parameters together on a tool page
2) Put a separator in between related groups.
I have a tool with lots of parameters. It's ok to have them all on one
page but I'd like to have some space or a line between the
Hi John,
On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote:
On 08/15/2012 08:59 PM, Dan Tenenbaum wrote:
Hi all,
I'm trying to wrap my head around what the conditional tag does...it
looks like it doesn't do what I would like.
I want to create a tool that allows
On Thu, Aug 16, 2012 at 10:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi John,
On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote:
On 08/15/2012 08:59 PM, Dan Tenenbaum wrote:
Hi all,
I'm trying to wrap my head around what the conditional tag does...it
looks like
Hi John and Peter,
On Thu, Aug 16, 2012 at 11:37 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Aug 16, 2012 at 6:53 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi John,
On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote:
Hello Dan,
The easiest way to go
Hi all,
I'm trying to wrap my head around what the conditional tag does...it
looks like it doesn't do what I would like.
I want to create a tool that allows the user to upload a data file and
then have it run through one or more filters. Each filter takes one or
more parameters.
I was thinking
/2012 11:56 PM, Dan Tenenbaum wrote:
Apologies for originally posting this to galaxy-user; now I realize it
belongs here.
Hello,
I'm a galaxy newbie and running into several issues trying to adapt an
R script to be a galaxy tool.
I'm looking at the XY plotting tool for guidance
(tools
On Wed, Apr 25, 2012 at 9:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hello Hans-Rudolph,
On Wed, Apr 25, 2012 at 1:37 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Dan
There seems to be several issues connected with each other or not, I don't
know.
- Let's start with the 'curiosity
On Wed, Apr 25, 2012 at 11:48 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Wed, Apr 25, 2012 at 9:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hello Hans-Rudolph,
On Wed, Apr 25, 2012 at 1:37 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Dan
There seems to be several issues connected
Apologies for originally posting this to galaxy-user; now I realize it
belongs here.
Hello,
I'm a galaxy newbie and running into several issues trying to adapt an
R script to be a galaxy tool.
I'm looking at the XY plotting tool for guidance
(tools/plot/xy_plot.xml), but I decided not to embed
On Tue, Apr 24, 2012 at 9:16 AM, Hui Zhao zh...@cbio.mskcc.org wrote:
Hi,
This is Julia from Memorial SLoan-Kettering Cancer Center. I've been using
the galaxy Cloudman instance last year and it worked fine. But today when I
tried to launch instance galaxy-cloudman-2011-03-22(ami-da58aab3).
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