Hi John,
One more problem with multifile upload - when I display a workflow which
includes multi upload tool, I get:
Module workflow_run_mako:476 in render_row_for_param
http://140.79.7.98/workflow/run?id=f597429621d6eb2b
__M_writer(unicode(param.get_label()))
AttributeError:
Hello,
Some Galaxy tools failed to import rpy module and displays the following
message:
Traceback (most recent call last):
File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py, line
5, in module
from rpy import *
ImportError: No module named rpy
For instance, the
Hi Sarah
you need to install the rpy module:
http://rpy.sourceforge.net/rpy.html
As a warning: we have been struggling to get rpy to work with newer
versions of R. In or experience in only works with R version 2.9 and
older. Thanks to a recent effort of our sysadmin, we can now use it with
On Wed, Jun 5, 2013 at 9:42 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Sarah
you need to install the rpy module:
http://rpy.sourceforge.net/rpy.html
As a warning: we have been struggling to get rpy to work with newer versions
of R. In or experience in only works with R version 2.9 and
On Wed, Jun 5, 2013 at 8:56 AM, alex.khassa...@csiro.au wrote:
Hi John,
One more problem with multifile upload – when I display a workflow which
includes multi upload tool, I get:
Module workflow_run_mako:476 in render_row_for_param
__M_writer(unicode(param.get_label()))
AttributeError:
Thanks a lot for these explantions,
I have downloded refactored tools (rpy2 is more suited to our R version).
Unfortunatly, galaxy still do not import rpy2 ..
Traceback (most recent call last):
File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py, line
6, in module
Hi Peter,
Of course I added def get_label(self), as a matter of fact, I copied
get_label() from ToolParameter class. That's why I'm a bit confused.
The get_label function returns a string which is supposed to be displayed, but
instead something is trying to execute it?
Best Regards,
Alex
On Wed, Jun 5, 2013 at 12:21 PM, alex.khassa...@csiro.au wrote:
Hi Peter,
Of course I added def get_label(self), as a matter of fact, I copied
get_label() from ToolParameter class. That's why I'm a bit confused.
The get_label function returns a string which is supposed to be displayed,
If you don't have pull request 122 in your code base, you will want to add it:
https://bitbucket.org/galaxy/galaxy-central/pull-request/122/add-optional-upload-attribute-to-tool/diff
Then, all you need to do is add the attribute '
workflow_compatible=false ' to your top level tool XML element in
Three quick comments on this thread:
- A real short-coming of my colleague JJ is that he doesn't possess a
tenth the ego that I do, so he doesn't care, but I think it is
important he gets credit. He did 85% of the work, and the harder 85%
at that, so they should be called the JJ changes.
- It is
On Wed, Jun 5, 2013 at 2:18 PM, John Chilton chil...@msi.umn.edu wrote:
Three quick comments on this thread:
- A real short-coming of my colleague JJ is that he doesn't possess a
tenth the ego that I do, so he doesn't care, but I think it is
important he gets credit. He did 85% of the work,
On 06/05/2013 03:33 PM, Peter Cock wrote:
On Wed, Jun 5, 2013 at 2:18 PM, John Chilton chil...@msi.umn.edu wrote:
//
- Finally, an idea - Death to RPY - The BoF. Everyone with a stake
in this meets with laptops at the Galaxy conference together and we
divvy up the remaining tools to
Hi Greg,
I just updated our instance:
hg pull
hg update
sh manage_db.sh upgrade
and checked the current version
parent: 9944:cea3ddf6cdda tip
Update tag for stable_2013.06.03
Zweig: stable
Ãbernehme: 16 unbekannt (clean)
Aktualisiere: (aktuell)
Subsequently, I tried again and it took a
Any ideas?
Thanks!
On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:
Suppose a tool didn't have any kind of configuration and therefore didn't
need to be displayed in the Analyze Data part of Galaxy. Is there a way to
modify tool_conf.xml so that a particular tool is only
On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:
Suppose a tool didn't have any kind of configuration and therefore didn't
need to be displayed in the Analyze Data part of Galaxy. Is there a way
to modify tool_conf.xml so that a particular tool is only displayed in the
Hi. I am new to the Galaxy forum and I am trying to setup a new local
Galaxy instance with MySQL on RH6.2 x86_64.
On a newly installed OS node, using the hg clone command (hg clone
https://bitbucket.org/galaxy/galaxy-dist#stable) which gets the current
Galaxy 20130603 image, I am getting the
Peter,
Thanks for getting back to me.
I'm working on an existing project where my predecessors have added a tool that
enables a user to add REST and SOAP Web services as usable tools within Galaxy
by providing their WSDL or WADL URLs. It makes sense that the tools that are
added should show
Hi Linda,
The decorator issue should be resolved in galaxy-central now. I'm setting
up a test environment to see if I can reproduce the mysql issue now, and
will let you know what I come up with.
Thanks!
-Dannon
On Wed, Jun 5, 2013 at 11:12 AM, Linda Cham lc...@us.ibm.com wrote:
Hi. I am
Add workflow_ compatible =false to the tool XML element to hide it
in the workflow editor. Check the tools/data_source/upload.xml for an
example of this.
If you would like to hide it both in the workflow editor and the side
bar but still allow for other direct links to it you can setup dynamic
This is great! Will it work with sections as well?
Thanks!
Sincerely,
Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA TA, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu
On Wed, Jun 5, 2013 at 4:37 PM, Michael E. Cotterell
mepcotter...@gmail.com wrote:
Peter,
Thanks for getting back to me.
I'm working on an existing project where my predecessors have added a tool
that enables a user to add REST and SOAP Web services as usable tools within
Galaxy by
Yes to the toolbox filters, no the dynamic job destinations (these
need to be configured per tool).
Look at the last example included with the pull request -
per_host_tool_sections for an example of how to configure tool section
filters.
-John
On Wed, Jun 5, 2013 at 10:51 AM, Michael E.
Hi All,
Just did an update to HEAD, and upon restarting the daemons received
the following messages:
galaxy.jobs.handler DEBUG 2013-06-05 10:55:31,478 recovering job 2083 in
condor runner
Traceback (most recent call last):
File
John,
Is there a way to hide an entire section (not just make it greyed out) using
the most recent galaxy-dist?
I'm investigating the pull request you linked to, and it looks interesting, but
is it compatible with galaxy-dist (it's on the bitbucket page for
galaxy-central)?
Thanks!
If you look at the date on the pull request it looks like it was a
full month before they even froze central for the last dist release,
so at this point I would be more confident it is going to work with
galaxy-dist than galaxy-central.
-John
On Wed, Jun 5, 2013 at 11:04 AM, Michael E. Cotterell
Excellent.
Is there an example of a modified universe_wsgi.ini file like the one mentioned
in the description of the pull request?
Sincerely,
Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA TA, University of Georgia
I was able to work around this error by hacking the condor job runner,
there were two obvious errors. First, in recover(), galaxy_id_tag was
not being set (hence the NameError). Second, the same method was
invoking self.__old_job_state with one argument when it clearly expects
two. The
Hi,
Our lab is in the process of installing a local version of Galaxy on a
computer with the following specs:
- Mac Pro mid-2012
- OS X 10.8.3
- 2 2.4 GHz Intel Xeon Processors
- 6 cores per processor, 12 cores total
- 64 GB RAM
This installation is meant to be used by a single user. We
On Jun 5, 2013, at 2:11 PM, Branden Timm wrote:
I was able to work around this error by hacking the condor job runner, there
were two obvious errors. First, in recover(), galaxy_id_tag was not being
set (hence the NameError). Second, the same method was invoking
self.__old_job_state with
Hi Dannon,
Thanks. I tried to do the hg pull and update and hg tip but I do not see
the changes in my working directory. So I added the one liner eggs.require
( decorator ) to scripts/manage_db.py.
Ran the sh manage_db.sh upgrade and get this error:
File
Hi Linda,
Hi Dannon,
Thanks. I tried to do the hg pull and update and hg tip but I do not
see the changes in my working directory. So I added the one liner
eggs.require( decorator ) to scripts/manage_db.py.
Ran the sh manage_db.sh upgrade and get this error:
that is really strange. Can
Hi Bjorn,
Currently seen
$ hg tip
changeset: 9850:cea3ddf6cdda
branch: stable
tag: tip
user:Nate Coraor n...@bx.psu.edu
date:Mon Jun 03 16:17:31 2013 -0400
summary: Update tag for stable_2013.06.03
Removed galaxy-dist directory and rerun the hg clone command.
1. We want to use the NGS:Mapping tool 'Map with Bowtie for Illumina'
which requires 'bowtie (0.12.7) with bowtie indexes'. Do we simply
download the bowtie software, place it into
/Users/administrator/galaxy-dist/tools, restart Galaxy, and the tool
is available under NGS:Mapping ?
Correct,
Hi,I am trying desperately to setup my GALAXY system so that if you enter the website, you need to authenticate yourself using the proxy setup...I also would like to be able to BYPASS the proxy server when an API call is made...In the example proxy setting I have setup in the following
Why not use Allow All / Deny All rules?
Location /
... your Auth Type stuff here ...
Deny from all
Allow from 127.0.0.1 # Assuming API calls are made locally
Satisfy any
/Location
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer
Hi all,
I've been trying to get my velvet optimiser wrapper to automatically
install the tool and its dependencies to no avail.
Here is my problem in detail.
I have what I thought would be a simple wrapper and tool to pack into the
new toolshed.
I have a tool_wrapper which points to a perl
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