Hi DK,
Looking at your XML that looks OK.
It might not be important, but how exactly are you running planemo
test?
I'm asking because currently it will not create tool-data/twobit.loc
for you from your sample file - although in that case I would have
expected a different error message:
https://
Hi D K,
for a good example of how to test parameters from data tables, please
see:
https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers
Your tool_data_table_conf.xml.test should be different from your .sample
and contain:
Please note the use of ${__HERE__} to i
Hello,
I have installed prokka, perl and bioperl in my Galaxy's ToolShed.
However, my users are getting this error during execution of prokka:
Can't locate Bio/Root/Version.pm in @INC (@INC contains: /usr/local/lib64/perl5
/usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
/usr/share/perl5/vend
Hello Community,
When I use the paste/fetch functionality to download data, the filename is
display as "Pasted Entry" into my history panel.
Is it possible to indicate the filename I would like to be display into the
history before the download ? I can see an edit button into the upload
window bu
Hi Peter,
This is the command I'm using to run planemo:
. galaxy_test/.venv/bin/activate
planemo test --test_data /home/galaxy-functional-testdata --galaxy_root
galaxy-test/ --skip_venv test.xml
I'm getting no errors when using the planemo lint tool.
Thanks!
On Fri, Oct 7, 2016 at 2:06 AM, Pete
Good, because you are using planemo test --galaxy_root ...
you can preset the *.loc files as needed (because currently
Planemo will not do this for you).
See also Nicola's reply.
Peter
On Fri, Oct 7, 2016 at 5:49 PM, D K wrote:
> Hi Peter,
>
> This is the command I'm using to run planemo:
> . g
Hi Nicola,
Thanks for the response, I'm still getting the same issue though. I've
followed the set up you've shown for bowtie_wrappers but am getting the
same error.
I've changed my file structure to look like this:
tmp/test.xml:
>
>
>
>
> ...
>
>
>
>
>
Hi All,
Computer demo submissions for Plant and Animal Genome are due October 28.
See below for details.
Galaxy will again have a presence at PAG. The two-hour Galaxy workshop on
Tuesday will likely focus on genome annotation, and several other proposals
are in the works.
PAG is in San Diego in
Hi D K,
I think that the problem may be that the table name is different in your
test.xml , tool_data_table_conf.xml.sample and
tool_data_table_conf.xml.test files (type_indexes, twobit_indexes and
twobit respectively), should always be twobit.
Cheers,
Nicola
On 07/10/16 18:04, D K wrote:
H
Thanks Nicola,
That fixed it when all of the files are in the tmp/ directory
Is this file/directory structure required when doing this?
When I try putting the relevant entries in
"galaxy-test/tool_data_table_conf.xml.test" and
"galaxy-test/tool_data_table_conf.xml.sample" and the "twobit.loc" i
Hi Edgar,
presently the Prokka wrapper requires some dependencies (in particular
some Perl modules) to be installed separetely, see the README file at
https://toolshed.g2.bx.psu.edu/view/crs4/prokka/
We are planning to release an updated Prokka wrapper which will use
Conda dependencies, you c
Hi all,
I’m working on setting up a Galaxy server for use with speech and language
data. While I can probably get there myself eventually, I’m thinking it would
be good to get some (paid) help if it were available.
If you have some experience setting up a public facing Galaxy instance, and yo
Hi Steve,
make sure to check out https://wiki.galaxyproject.org/Events
There are 2 extensive admin trainings going to happen in near future.
November in Salt Lake City and February in Melbourne.
Martin
On Fri, Oct 7, 2016 at 4:23 PM Steve Cassidy
wrote:
> Hi all,
> I’m working on setting up
Hi Steve,
I wish I could assist you a little bit. But what I can do is to get in
touch with Pieter Lukasse (pie...@thehyve.nl) from Hyve: http://thehyve.nl/
Pieter is the Galaxy expert in this company and he rocks! Maybe you can
figure something out.
Ciao and have a nice weekend!
Bjoern
Am 07.1
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