Hi,
I've got a strange problem with python paths/eggs. When I run any tool that
produces html/text output I get the error:
WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be
fetched.
So if I close galaxy, delete the eggs folder, run fetch_eggs.py (on the
cluster,
Hi all,
Could someone comment on my question below ? I see that a similar question from
Eric (with title object_store_conf.xml route users to different storage ) is
also unanswered.
Thanks for your help,
Pieter.
From: galaxy-dev-boun...@lists.bx.psu.edu
I have CEAS as a tool. I wrapped the standalone CEAS version. I tried adding a
binary datatype for the annotation db but even with the binary datatype upload
somehow did not work (IIRC galaxy tried to convert it to ascii).
I then put the database as a selectable parameter in a dropdown list,
Hi,
I've been poking around a bit more. It looks as though galaxy isn't actually
downloading and installing the tools. The tool status changes to installed in
the web interface and postgres but the tool is not present on disk. The log
below shows no download and make of the tool and
An answer may not be forthcoming because it is easier to say something
is possible then to say it is impossible. I will risk embarrassment
however and say there is not a configuration file in Galaxy to support
this, there is not an alternative solution at this time that I am
aware of. I really
Thanks for the bug report, that is indeed a problem - I am not sure
how the torque runner here would ever reach a complete job state. I
prefer the following fix however, if you would be willing to verify it
fixes the problem you are encountering I would be happy to apply it to
Galaxy's stable
Hello Briand,
This may take some back-and-forth with you to understand the steps you have
taken so far. Successfully installing a repository that contains tools usually
results in the tools being displayed in the Galaxy tool panel. However, there
may be issues that result in the tools not
Hi Joe,
Something is automatically re-fetching the Python 2.6 eggs? Is the
Galaxy server itself using 2.6 perhaps?
--nate
On Fri, Feb 28, 2014 at 3:42 AM, Joseph Ward j.x.w...@dundee.ac.uk wrote:
Hi,
I've got a strange problem with python paths/eggs. When I run any tool that
produces
Hi Nate,
This is the confusing thing. I've check the python versions and python path
of the vm running galaxy and where the jobs are run and it's 2.7 across the
board. I submit the script that fetches the eggs to the cluster using the
same environment as the jobs are submitted in. I was just
Dear Sir or Madam,
I am working for the University of Westminster on the ER-Flow project
(http://www.erflow.eu/home). I'm currently investigating a way to use the
galaxy workflow engine with a command line interface in order to support it
within our project.
The idea would be to develop a
Respected Sir,
I don't think so that problem is in tool, because when I run same tool of
normal terminal, it generate output.
What I am thinking is:
Consider Galaxy is running from its own directory, my files are in
*/home/user/Documents/*
While uploading file, I am choosing for Link to files
Dear Benoît Meilhac,
In my plugin, I would have to import the workflow, then run it with inputs
listed in the executable command line, and after a successful execution, I
would have to retrieve the outputs generated, then delete the created
workflow and any files related that exist.
The
The current code in: lib/galaxy/tools/parameters/dynamic_options.py
only searches the top layer of the dict to find the dependency value.
A fix is provide in pull request:
#343: Need to traverse the other_value dict to find dependencies for ParamValueFilter
Hello Benoît,
I remember seeing projects trying to do something similar (store workflows
internally and execute on Galaxy), like http://refinery-platform.org/, so
it could be useful to take a look there too. I've been trying to do
something similar but with the Java interface to the Galaxy API
Hi,
No joy on the migration strategy. Deseq is example of a tool that I installed
successfully yesterday. Bowtie2 is an example of a tool that isn't showing up
even though the web interface indicates that it is successfully installed.
Here is my directory structure relating to bowtie2:
$
Hello all,
Find out what's happening in the
Galaxyhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03
! The March 2014 Galaxy
Updatehttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03
include is out and highlights include:
-
54 new
Hello Sheldon,
What is the configuration setting you are using for the location to install
repositories? This is defined by the tool_path attribute of the toolbox tag
in your shed_tools_conf.xml file. The default is:
toolbox tool_path=../shed_tools
On Feb 28, 2014, at 3:47 PM, Briand,
Hi,
Yep that's what I have.
Here is deseq:
find . -name *deseq*
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts
./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts
Hi Greg,
Also for bowtie2. I can confirm that it doesn't have an entry in the
shed_tool_conf.xml file. Sorry I didn't mention these before. Its been a long
week and there obviously was a problem between my chair and keyboard. :)
-Sheldon
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