Hi Bjoern,
I've just done some more testing of my tool with a fresh install and a fresh
checkout of galaxy. After install of this tool
http://testtoolshed.g2.bx.psu.edu/view/iracooke/package_protk_1_2_5
I have an env.sh that looks like
GEM_PATH=/home/vagrant/tool_dependencies/protk/1.2.5/ira
I believe this is fixed in 11184:d2b9f616e66c - at least everyting worked for
me. However, committing to next-stable was a bit tweaky although I think all
is ok. Please let me know if you see any problems.
Thanks!
Greg Von kuster
On Oct 30, 2013, at 4:09 PM, John Chilton wrote:
> I can ver
Moving this over to galaxy-...@bx.psu.edu, the best list for tool design
questions. Best! Jen, Galaxy team
On 10/30/13 2:24 PM, dam...@learningpoint.ca wrote:
Has anyone run into this? I'm building a general-purpose filter
control on my galaxy tool xml template for enabling numeric fields to
Hi Peter,
Thanks for the zippy response. I had failed to previously install those
wrappers at all, it looks like. I copied my galaxy-dist folder to another host
to test and forgot to install some of the shed tools.
Much appreciated!
Carrie Ganote
From:
Hi Eric,
I've being pondering this too - it can easily get very complicated
with multiple copies of a workflow with minor variations.
I agree that "read only" sharing makes sense as a short term
goal, but I see two variants being useful here - an read only
snapshot copy from the instant it was sh
On Wed, Oct 30, 2013 at 9:22 PM, Ganote, Carrie L wrote:
> Hi List,
>
> It seems that the blastdb and blastdbp data format is not respected on my
> local install; is it just not generally defined, or am I missing something
> in /lib/galaxy/datatypes or in datatypes_conf?
>
> The most recent blasp
On Wed, Oct 30, 2013 at 3:58 PM, Björn Grüning
wrote:
> Hi John & Greg,
>
> yes I can confirm that. Thanks for reproducing.
>
> Btw. should I set up one test repository for every feature (lets say for
> ruby and R) that will stay like it is and function as test environment.
> Or should be write so
Hi John & Greg,
yes I can confirm that. Thanks for reproducing.
Btw. should I set up one test repository for every feature (lets say for
ruby and R) that will stay like it is and function as test environment.
Or should be write some unit tests for it?
Thanks,
Bjoern
> Thanks John,
>
> I just s
Hi List,
It seems that the blastdb and blastdbp data format is not respected on my local
install; is it just not generally defined, or am I missing something in
/lib/galaxy/datatypes or in datatypes_conf?
The most recent blasp wrapper includes this for the input parameter:
type="data" format="b
Thanks John,
I just sent my message as yours arrived - this will help me more quickly
resolve the issue. I'll have a fix soon.
Greg Von Kuster
On Oct 30, 2013, at 4:09 PM, John Chilton wrote:
> I can verify augustus doesn't work correctly any longer, but I do not
> get the same error. The pa
Hello Bjoern,
Can you confirm that you have the following status for your tool dependencies
when you attempt to install your augustus repository from the main tool shed?
I haven't tracked down the reason that the AUGUSTUS_SCRIPT_PATH dependency is
in the Never installed state. Is this depende
I can verify augustus doesn't work correctly any longer, but I do not
get the same error. The package installs properly but set_environment
doesn't get handled.
As far as I can tell this changeset:
https://bitbucket.org/galaxy/galaxy-central/commits/ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877
Would
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
I'm working with a number of people in my department to develop a single
workflow that will be used for a course we teach. So far I've found that
"sharing" a workflow with individual users/roles isn't very optimal.
They email me with changes they'd lik
Hi Bjoern,
I'll test, but I wonder if the problem is that GEM_PATH is set instead of
GEM_HOME. I think GEM_HOME needs to be set also. It's zoo of environment
variables out there :)!!
Also ... I think GEM_HOME should be set using "set_to" not "prepend_to" ...
I am using the latest galaxy
On Wed, Oct 30, 2013 at 6:02 PM, John Chilton wrote:
> I am pretty confident this worked at some point, this is potentially a
> regression of some kind (or I am crazy person). I will try to find
> time to take a closer look.
OK, likewise - I'll try to put together a reproducible test case,
and tr
Hi Ira,
> Hi Bjoern,
>
> I'll test,
thanks!
> but I wonder if the problem is that GEM_PATH is set instead of GEM_HOME. I
> think GEM_HOME needs to be set also. It's zoo of environment variables out
> there :)!!
Mh according to
http://stackoverflow.com/questions/11277227/whats-the-dif
I am pretty confident this worked at some point, this is potentially a
regression of some kind (or I am crazy person). I will try to find
time to take a closer look.
I have created a Trello card for this:
https://trello.com/c/9knsbvmx
Sorry about that!
-John
On Wed, Oct 30, 2013 at 12:35 PM, P
Hi John,
I've just tried a workflow using my MIRA4 de novo wrapper:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
To keep it simple, in this example I just had two input FASTQ
files, the forward and reverse files for paired end MiSeq data.
This seemed to work fine for re-running
Hello all,
This is just to announce I am working on a wrapper for
"CLC Assembly Cell" which is the CLCbio commercial
command line assembly tool suite.
http://www.clcbio.com/products/clc-assembly-cell/
Our institute bought a licence primarily for use on plant
genomes where other assemblers at the
Hi Greg,
sorry for the confusion. You answered to Saskia
>>> This was indeed a bug (not "abut" which was a spell checker spelling
>>> error) which has been resolved in 6:83bed9c7dbbc. This fix has
If I search for that number I only find your fix for the repository
action view. But I'm searc
Hello Bjoern,
The changeset to which your link refers is the change that allows anyone that
has write permission on a repository to reset all metadata on that repository
from the "Repository Actions" pop-up menu on the "View repository" page.
Previous to this change, this feature was restricte
Hi Bjoern,
Indeed resetting the metadata solved the problem. Thanks!
Best regards,
Pieter.
-Original Message-
From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
Sent: woensdag 30 oktober 2013 15:16
To: Lukasse, Pieter
Cc: Greg Von Kuster (g...@bx.psu.edu); galaxy-...@bx.psu.edu
S
Hi Pieter,
I tried to reproduce it and looked over your files. I also tried to
reproduce it and can't. For me its showing up nicely:
http://testtoolshed.g2.bx.psu.edu/view/bgruening/upload_testing
So please try to reset metadata of that repository. And hopefully your
issues are gone magically :
Hi Ira,
that is strange, because PATH and GEM_HOME should be set automatically
for you.
Please have a look at
https://github.com/bgruening/galaxytools/blob/master/orphan_tool_dependencies/package_ruby2_bioruby_1_4/tool_dependencies.xml
http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_ruby
Hi Greg,
The strange thing is that the tool loads fine in my local Galaxy server (so not
using toolshed but the old-fashioned way). The difference could be that my
Galaxy server is not up to date and perhaps using a different xml parsing
scheme?
Anyway, are there XSD files which I could use t
Hi Yaron
This is useful - Thank you very much.
Coming up with such a sql statement to identify the files from people
who have left our institute has been on my list of things to do for
quite some time.
Now I just need to figure how to distinguish the files which have been
shared with people
On Thu, Oct 17, 2013 at 4:28 PM, Peter Cock wrote:
> On Thu, Oct 17, 2013 at 4:05 PM, Eric Rasche wrote:
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> Peter,
>>
>> On 10/17/2013 07:58 AM, Peter Cock wrote:
>>> On Fri, Oct 4, 2013 at 2:24 PM, Peter Cock
>>> wrote:
On Fri, Oct 4,
Hi.
During IT housekeeping, we have decided that we must know the filenames
of all of the galaxy datasets in our local deployment. Searching the docs
and
the web yielded no reasonable answer, so we figured we'll just write our
own tool.
At first, we thought about a Galaxy tool, but found no way to
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