Re: [galaxy-dev] Help wanted: setting up a production server

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

Re: [galaxy-dev] Help wanted: setting up a production server

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, >

[galaxy-dev] Help wanted: setting up a production server

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

Re: [galaxy-dev] galaxy - bioperl - prokka

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

Re: [galaxy-dev] planemo test with

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"

Re: [galaxy-dev] planemo test with

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:

[galaxy-dev] Fwd: [mailinglist] Call for Submissions: Computer Demo Track at PAGXXV.

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

Re: [galaxy-dev] planemo test with

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: > > > > > ... > > > > >

Re: [galaxy-dev] planemo test with

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

Re: [galaxy-dev] planemo test with

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,

[galaxy-dev] Paste/Fetch data, indicate filename before download data (default = Pasted Entry)

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

[galaxy-dev] galaxy - bioperl - prokka

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

Re: [galaxy-dev] planemo test with

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

Re: [galaxy-dev] planemo test with

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: