Hi JJ,
I think this is a great idea.
Do you want to make the pull request for this? Or I can merge it into my fork
if you like.
Cheers
Ira
On 26 Jul 2014, at 3:22 am, Jim Johnson johns...@umn.edu wrote:
Ira,
Thanks for getting a sqlite datatype into galaxy. I was wanting to
On 30/10/2013, at 3:51 PM, Ira Cooke iraco...@gmail.com wrote:
Hi Bjoern,
Changing the title to reflect the proper topic
I see now that the gem executables are installed under $INSTALLDIR/bin so I
added this to the environment for my protk install.
That got me to the point where my
//environment_variable
/action
In my protk tool definition.
RUBYLIB isn't set ... hopefully this will not be an issue since I guess
that's mostly just needed for Gem installation/compilation.
This part works now :)
Thanks
Ira
On 30/10/2013, at 3:51 PM, Ira Cooke iraco...@gmail.com
clarify.
Thanks
Ira
On 31/10/2013, at 6:06 AM, Ira Cooke mudflatsoftw...@gmail.com wrote:
Hi Bjoern,
I saw the same SO post ... but it says that GEM_PATH can be multiple paths
but one of them should be GEM_HOME. Under your system (I think) GEM_HOME
remains unset?
Anyway
Ahhh ... Thanks .. I can't believe I missed that. Thanks for spotting it.
I'm not sure I understand enough about how this works to answer your ruby_home
question. Ill play with this more tomorrow and see how things work with my
tools and maybe have more feedback then
Cheers
Ira
On 29 Oct
Hi Bjoern,
Changing the title to reflect the proper topic
I see now that the gem executables are installed under $INSTALLDIR/bin so I
added this to the environment for my protk install.
That got me to the point where my executable would run ... but now I'm seeing
that in my env.sh file I
Hi All,
The short version of my problem is that I often seem to find myself in a
situation where my tool gets stuck in the Installing phase ... and I don't
know how to get feedback on it to see where it is failing. What I guess I'm
after is just the stdout of the tool installation .. but
Hi Bjoern,
Thanks ... I thought I had to do that in order to make the GALAXY_RUBY_HOME
variable available ... nice that it's not necessary.
I've updated the tool on the test toolshed and have rerun my test but
unfortunately the problem is still there.
Cheers
Ira
On 29/10/2013, at 10:06 AM,
Dear All,
The galaxy community now has a mailing list dedicated to proteomics. If you're
using galaxy to do proteomics, or if you are thinking of doing so then this
list if for you.
In case you missed it, there is also a proteomics wiki page at
http://wiki.galaxyproject.org/Proteomics
To
the
functional test framework will recognize it. The syntax is very nearly the
same:
export GALAXY_TOOL_DEPENDENCY_DIR=/home/iracooke/tool_dependencies ; sh
run_functional_tests.sh -installed
--Dave B.
On 6/3/13 00:25:53.000, Ira Cooke wrote:
Hi Dave,
Just following up on this (now
is documented in https://trello.com/c/eVT3QWJF
--Dave B.
On 5/8/13 20:08:08.000, Ira Cooke wrote:
Hi All,
I'm starting to add functional tests to my tools but I've found that I can't
get the test framework to work well with tool dependencies.
The tool I'm considering is xtandem
http
like a failure compiling ruby ... but it's hard to know what's missing
to fix it.
Cheers
Ira
On 14/05/2013, at 6:54 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, May 14, 2013 at 3:32 AM, Ira Cooke iraco...@gmail.com wrote:
Hi All,
My guess is that one of the most common ways
Hi All,
My guess is that one of the most common ways in which tools will fail tests on
the build-bot is when a dependency fails to install properly. I think this is
what is happening to my tool xtandem
http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem
One potential improvement that I
, Peter Cock wrote:
On Thu, May 2, 2013 at 10:24 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Thu, May 2, 2013 at 7:16 AM, Ira Cooke iraco...@gmail.com wrote:
Hi all,
I've written a script to help deal with the problem of maintaining
toolshed tools
across multiple toolsheds (eg test
Hi all,
I've written a script to help deal with the problem of maintaining toolshed
tools across multiple toolsheds (eg test and release)
The problem I encountered was that switching between test and production
versions of a suite of tools can be quite painful because every repository
a bit of time to figure out and resolve, but I'll let you know
as soon as we uncover and resolve the problem.
Thanks!
Greg Von Kuster
On Mar 5, 2013, at 1:49 AM, Ira Cooke wrote:
Hi,
I've just uploaded a set of updates to my proteomics tools on the toolshed.
These contain my
Hi,
I've just uploaded a set of updates to my proteomics tools on the toolshed.
These contain my best attempt to implement automatic dependency installation
... and for the most part it seems to work.
I have encountered the following issues though
(1) I don't see any way to ensure that one
it.
On 05/03/2013, at 9:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Mar 5, 2013 at 6:49 AM, Ira Cooke iraco...@gmail.com wrote:
Hi,
I've just uploaded a set of updates to my proteomics tools on the toolshed.
These contain my best attempt to implement automatic dependency
I was wondering whether the general policy is to keep the toolshed at
toolshed.g2.bx.psu.edu compatible with galaxy-dist or galaxy-central.
The reason I ask is that I went to install a tool from a production server I'm
trying to setup based on galaxy-dist ... but got an error;
The resource
filesystem have a look at
display_applications/genetrack.xml.
Thanks for using Galaxy,
Dan
On May 2, 2012, at 10:58 PM, Ira Cooke wrote:
Dear All,
Our toolshed tools include a custom display application. Although the
display application is open source (
https://bitbucket.org
On May 3, 2012, at 6:49 AM, Ira Cooke wrote:
Hi Dan and Greg,
Thanks for your answers on this. So far I have managed to make things work
following Dan's suggestion ... except that I can't seem to get my
configuration data file to install into tool-data. I'm not sure why this
might be since
Dear List,
I'm trying to check my toolshed tools by installing first on a local toolshed,
but running into an error every time I try to add my tools.
In order to rule out possible idiosyncracies of my system I've reproduced the
error on an Ubuntu VM ... the system was not completely clean
, 2012, at 7:20 AM, Ira Cooke wrote:
Hi Greg,
I'm afraid to say I might have been a bit ahead of myself in asking you to
create that Proteomics category. We're almost ready to upload our tools,
but at the last minute we've discovered a bunch of issues we need to sort
out. I'm
the 16th ... so I guess the
earliest our tools would be up is after the 16th.
Sorry about that. I hope you're OK with a 0 beside the Proteomics category for
now.
Ira
On 30/03/2012, at 10:03 AM, Ira Cooke wrote:
Thanks ... that would definitely be a good idea.
Well try to implement proper
.27s_functional_test_framework_to_test_tools_installed_into_your_local_Galaxy_instance
Greg
On Mar 29, 2012, at 6:53 PM, Ira Cooke wrote:
Dear Greg,
Thanks very much for that. I'll do a last proof-read of the tools and
upload later on today.
We're working on some better documentation ... to get it all working takes
some extra setup steps on the part
listen to advice from the community on this, but in the meantime,
proprietary datatypes and sniffers are loaded after those in the distribution.
Thanks for your patience and help on this issue.
Greg
On Feb 6, 2012, at 11:37 PM, Ira Cooke wrote:
Hi Greg,
As far as I know
fixed.
Greg
On Feb 7, 2012, at 6:16 PM, Ira Cooke wrote:
Hi Greg,
Thanks for that fix ... I'll check it out.
I think the issue of sniff order is a pretty important one for shed tools
that require proprietary datatypes. The problem is that galaxy's default
sniffers include some
Dear Greg,
In the latest version of the galaxy-central code there seems to be a bug
preventing me from updating my tools. When I go to update a tool I get the
following error
URL:
Hi,
We've been running into an issue when attempting to create a new toolshed tool.
We have the toolshed and the main galaxy web app setup and running, but
updating our tool to the latest version always fails.
When clicking Get updates on our installed tool we find that the initial
request
.
I'm not sure why we're having problems. It does seem to be specific to mac
though, as I can run this same checkout on linux without any workarounds.
~Mike
On Jun 21, 2011, at 11:47 PM, Ira Cooke wrote:
Hi,
I recently downloaded galaxy and had some problems installing it on my
Hi,
I recently downloaded galaxy and had some problems installing it on my machine
(running Mac OSX 10.6.7 ). I've found a workaround to my problem, but I
thought I should post here in case it is useful.
I obtained the standard galaxy distribution using
hg clone
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