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

[Björn Grüning]

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 07.10.2016 um 22:30 schrieb Martin Čech:
> 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 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 you have some time available in the next couple of
> weeks, please get in touch.  
> 
> Any location is probably ok as long as we can work out how to
> reimburse you.  We (and the servers) are based in Australia but I’m
> currently in New York.  
> 
> Thanks,
> 
> Steve
> 
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
> 
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> 
> 
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Re: [galaxy-dev] Help wanted: setting up a production server

[Martin Čech]

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 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 you have some time available in the next couple of weeks, please get in
> touch.
>
> Any location is probably ok as long as we can work out how to reimburse
> you.  We (and the servers) are based in Australia but I’m currently in New
> York.
>
> Thanks,
>
> Steve
>
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
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>   https://lists.galaxyproject.org/
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>   http://galaxyproject.org/search/mailinglists/
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[galaxy-dev] Help wanted: setting up a production server

[Steve Cassidy]

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 you 
have some time available in the next couple of weeks, please get in touch.

Any location is probably ok as long as we can work out how to reimburse you.  
We (and the servers) are based in Australia but I’m currently in New York.

Thanks,

Steve

—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

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

[Nicola Soranzo]

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 can track the progress at:


https://github.com/galaxyproject/tools-iuc/pull/985

Cheers,
Nicola

On 07/10/16 15:06, Fernandez Edgar wrote:


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/vendor_perl 
/usr/lib64/perl5 /usr/share/perl5 .) at 
/home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/prokka/1.11/crs4/prokka/f5e44aad6498/bin/prokka 
line 29. BEGIN failed--compilation aborted at 
/home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/prokka/1.11/crs4/prokka/f5e44aad6498/bin/prokka 
line 29.


I was under the impression that the galaxy’s tools will use the 
internal perl.


Do I just need to install Bio::Root:Version on my system installation 
of perl?


Please give me whatever information you can on this issue.

Regards,

*Edgar Fernandez*

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la 
Communication*//*


*/Université de Montréal/*

*//*

PAVILLON ROGER-GAUDRY, bureau X-210

(Bur. : *1-514-343-6111 poste 16568//*



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Re: [galaxy-dev] planemo test with

[D K]

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" in
"galaxy-test/test-data" and "galaxy-test/tool-data" then I get the same
error again. I'd like to be able to put the files here instead of in their
own directory structure.

Thanks!

On Fri, Oct 7, 2016 at 10:04 AM, D K  wrote:

> 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:
>
>>  
>>   
>>   
>> 
>> ...
>>   
>>   
>> 
>>  
>>   
>
>
> tmp/tool_data_table_conf.xml.sample:
>
>> 
>> 
>> value, path
>> 
>> 
>> 
>
>
> tmp/tool_data_table_conf.xml.test:
>
>> 
>> 
>> 
>> value, path
>> 
>> 
>> 
>
>
> tmp/tool-data/twobit.loc
>
>> hsapiens   /nfs/seqdata/reference_genome/
>> MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
>
>
> tmp/tool-data/twobit.loc
>
>> #
>
>
> tmp/test-data/twobit.loc
>
>> hsapiens   /nfs/seqdata/reference_genome/
>> MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
>
>
> Rather than placing these twobit.loc files etc... under tmp with test.xml
> I've also tried putting these files under galaxy-test/tool-data, test-data,
> etc... and that didn't help either.
>
> I'm not understanding what I'm doing wrong here. Any additional
> suggestions would be appreciated.
>
> Thanks!
>
> On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo 
> wrote:
>
>> 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 indicate the directory where the
>> tool is.
>> You should also have a comment-only tool-data/twobit.loc.sample , while
>> the loc file for testing should be in test-data/twobit.loc
>>
>> Cheers,
>> Nicola
>>
>>
>> On 06/10/16 23:08, D K wrote:
>>
>> Hi galaxy-dev,
>>
>> I'm having a problem running a test using planemo where I would like the
>> value of a parameter taken from one of the data tables. I get the following
>> error in planemo:
>>
>> 'Error creating a job for these tool inputs - Parameter refGenomeSource_type 
>> requires a value, but has no legal values defined.\n
>>
>>
>> From my script XML:
>>
>>>  
>>>   
>>>   
>>> 
>>> ...
>>>   
>>>   
>>> 
>>>  
>>>   
>>>
>>> From my "tool_data_table_conf.xml.sample" and
>> "tool_data_table_conf.xml.test" (mirrored)
>>
>>> >> allow_duplicate_entries="False">
>>> value, name, path
>>> 
>>> 
>>
>>
>> and from twobit.loc (where the columns are tab separated):
>>
>>> hsapiensH. sapiens (hg38)   /remote/RMS/users/galaxy/refer
>>> ence_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
>>
>>
>> Any suggestions would be greatly appreciated!
>>
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
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>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>>
>
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Re: [galaxy-dev] planemo test with

[Nicola Soranzo]

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:

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:

 
  
  

...
  
  

 
  


tmp/tool_data_table_conf.xml.sample:



value, path





tmp/tool_data_table_conf.xml.test:




value, path





tmp/tool-data/twobit.loc

hsapiens

/nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa


tmp/tool-data/twobit.loc

#


tmp/test-data/twobit.loc

hsapiens

/nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa


Rather than placing these twobit.loc files etc... under tmp with 
test.xml I've also tried putting these files under 
galaxy-test/tool-data, test-data, etc... and that didn't help either.


I'm not understanding what I'm doing wrong here. Any additional 
suggestions would be appreciated.


Thanks!

On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo > wrote:


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 indicate the directory where
the tool is.
You should also have a comment-only tool-data/twobit.loc.sample ,
while the loc file for testing should be in test-data/twobit.loc

Cheers,
Nicola


On 06/10/16 23:08, D K wrote:

Hi galaxy-dev,

I'm having a problem running a test using planemo where I would
like the value of a parameter taken from one of the data tables.
I get the following error in planemo:
'Error creating a job for these tool inputs - Parameter 
refGenomeSource_type requires a value, but has no legal values defined.\n

From my script XML:

 
  
  

...
  
  

 
  

From my "tool_data_table_conf.xml.sample" and
"tool_data_table_conf.xml.test" (mirrored)


value, name, path




and from twobit.loc (where the columns are tab separated):

hsapiens  H. sapiens (hg38)

/remote/RMS/users/galaxy/reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa


Any suggestions would be greatly appreciated!



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

[Dave Clements]

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 January.

Hope to see you there,

Dave C


-- Forwarded message --
From: Monica Munoz-Torres 
Date: Fri, Oct 7, 2016 at 3:15 AM
Subject: [mailinglist] Call for Submissions: Computer Demo Track at PAGXXV.
To: mailingl...@biocurator.org
Cc: Monica Munoz-Torres , Brian Smith-White <
smtwh...@ncbi.nlm.nih.gov>


Dear Colleagues,

*International Plant and Animal Genome XXV (PAGXXV)*
*January 14-18, 2017. San Diego, California, United States.*
http://intlpag.org/

PAGXXV will bring together more than 3,000 leading researchers in plant and
animal research, over 130 exhibits, more than 150 workshops, over 1000
posters, *and a computer demo track specifically designed to highlight
relevant software and online resources.* PAG is the largest Ag-Genomics
meeting in the world.

If you work on digital resources that enable life sciences research, please
consider submitting an abstract to the PAG Computer Demonstration Track.
Computer demos are 15 or 20 minutes long, and are an excellent way to get
resources in front of the people who will benefit the most from them.

*The Computer Demo abstract submission deadline is Friday October 28,
2016.  *

All computer demo presenters must be registered for the conference prior to
submitting.  Any software which is demonstrated at the PAG Conference must
also be available to the scientific community and non-commercial.

Visit http://www.intlpag.org/2017/abstracts/computer-demos for additional
information and to find a link to the submission form.


We hope to see you in San Diego!


*Monica Munoz-Torres and Brian Smith-White*
*PAGXXV Computer Demo Track Co-Chairs*

[image: Inline image 1]





-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720



-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
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Re: [galaxy-dev] planemo test with

[D K]

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:

>  
>   
>   
> 
> ...
>   
>   
> 
>  
>   


tmp/tool_data_table_conf.xml.sample:

> 
> 
> value, path
> 
> 
> 


tmp/tool_data_table_conf.xml.test:

> 
> 
> 
> value, path
> 
> 
> 


tmp/tool-data/twobit.loc

> hsapiens
> /nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa


tmp/tool-data/twobit.loc

> #


tmp/test-data/twobit.loc

> hsapiens
> /nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa


Rather than placing these twobit.loc files etc... under tmp with test.xml
I've also tried putting these files under galaxy-test/tool-data, test-data,
etc... and that didn't help either.

I'm not understanding what I'm doing wrong here. Any additional suggestions
would be appreciated.

Thanks!

On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo  wrote:

> 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 indicate the directory where the
> tool is.
> You should also have a comment-only tool-data/twobit.loc.sample , while
> the loc file for testing should be in test-data/twobit.loc
>
> Cheers,
> Nicola
>
>
> On 06/10/16 23:08, D K wrote:
>
> Hi galaxy-dev,
>
> I'm having a problem running a test using planemo where I would like the
> value of a parameter taken from one of the data tables. I get the following
> error in planemo:
>
> 'Error creating a job for these tool inputs - Parameter refGenomeSource_type 
> requires a value, but has no legal values defined.\n
>
>
> From my script XML:
>
>>  
>>   
>>   
>> 
>> ...
>>   
>>   
>> 
>>  
>>   
>>
>> From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test"
> (mirrored)
>
>> 
>> value, name, path
>> 
>> 
>
>
> and from twobit.loc (where the columns are tab separated):
>
>> hsapiensH. sapiens (hg38)   /remote/RMS/users/galaxy/
>> reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
>
>
> Any suggestions would be greatly appreciated!
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
>
>
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Re: [galaxy-dev] planemo test with

[Peter Cock]

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:
> . 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, Peter Cock 
> wrote:
>>
>> 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://github.com/galaxyproject/planemo/issues/530
>> https://github.com/galaxyproject/planemo/issues/530
>>
>> Is planemo lint happy with your tool?
>>
>> Peter
>>
>>
>> On Thu, Oct 6, 2016 at 11:08 PM, D K  wrote:
>>>
>>> Hi galaxy-dev,
>>>
>>> I'm having a problem running a test using planemo where I would like the
>>> value of a parameter taken from one of the data tables. I get the following
>>> error in planemo:
>>>
>>> 'Error creating a job for these tool inputs - Parameter
>>> refGenomeSource_type requires a value, but has no legal values defined.\n
>>>
>>>
>>> From my script XML:

  
   
   
 
 ...
   
   
 
  
   

>>> From my "tool_data_table_conf.xml.sample" and
>>> "tool_data_table_conf.xml.test" (mirrored)

 >>> allow_duplicate_entries="False">
 value, name, path
 
 
>>>
>>>
>>> and from twobit.loc (where the columns are tab separated):

 hsapiensH. sapiens (hg38)
 /remote/RMS/users/galaxy/reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
>>>
>>>
>>> Any suggestions would be greatly appreciated!
>>>
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>
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Re: [galaxy-dev] planemo test with

[D K]

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, Peter Cock 
wrote:

> 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://github.com/galaxyproject/planemo/issues/530
> https://github.com/galaxyproject/planemo/issues/530
>
> Is planemo lint happy with your tool?
>
> Peter
>
>
> On Thu, Oct 6, 2016 at 11:08 PM, D K  wrote:
>
>> Hi galaxy-dev,
>>
>> I'm having a problem running a test using planemo where I would like the
>> value of a parameter taken from one of the data tables. I get the following
>> error in planemo:
>>
>> 'Error creating a job for these tool inputs - Parameter refGenomeSource_type 
>> requires a value, but has no legal values defined.\n
>>
>>
>> From my script XML:
>>
>>>  
>>>   
>>>   
>>> 
>>> ...
>>>   
>>>   
>>> 
>>>  
>>>   
>>>
>>> From my "tool_data_table_conf.xml.sample" and
>> "tool_data_table_conf.xml.test" (mirrored)
>>
>>> >> allow_duplicate_entries="False">
>>> value, name, path
>>> 
>>> 
>>
>>
>> and from twobit.loc (where the columns are tab separated):
>>
>>> hsapiensH. sapiens (hg38)   /remote/RMS/users/galaxy/refer
>>> ence_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
>>
>>
>> Any suggestions would be greatly appreciated!
>>
>>
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>
>
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[galaxy-dev] Paste/Fetch data, indicate filename before download data (default = Pasted Entry)

[Floreline TOUCHARD]

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 but there is no action on click.



Thanks in advance,

Floreline
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[galaxy-dev] galaxy - bioperl - prokka

[Fernandez Edgar]

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/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at 
/home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/prokka/1.11/crs4/prokka/f5e44aad6498/bin/prokka
 line 29. BEGIN failed--compilation aborted at 
/home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/prokka/1.11/crs4/prokka/f5e44aad6498/bin/prokka
 line 29.


I was under the impression that the galaxy's tools will use the internal perl.
Do I just need to install Bio::Root:Version on my system installation of perl?
Please give me whatever information you can on this issue.

Regards,

Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
*  Bur. : 1-514-343-6111 poste 16568


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Re: [galaxy-dev] planemo test with

[Nicola Soranzo]

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 indicate the directory where the 
tool is.
You should also have a comment-only tool-data/twobit.loc.sample , while 
the loc file for testing should be in test-data/twobit.loc


Cheers,
Nicola

On 06/10/16 23:08, D K wrote:

Hi galaxy-dev,

I'm having a problem running a test using planemo where I would like 
the value of a parameter taken from one of the data tables. I get the 
following error in planemo:

'Error creating a job for these tool inputs - Parameter refGenomeSource_type 
requires a value, but has no legal values defined.\n

From my script XML:

 
  
  

...
  
  

 
  

From my "tool_data_table_conf.xml.sample" and 
"tool_data_table_conf.xml.test" (mirrored)



value, name, path




and from twobit.loc (where the columns are tab separated):

hsapiensH. sapiens (hg38)

/remote/RMS/users/galaxy/reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa


Any suggestions would be greatly appreciated!



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Re: [galaxy-dev] planemo test with

[Peter Cock]

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://github.com/galaxyproject/planemo/issues/530
https://github.com/galaxyproject/planemo/issues/530

Is planemo lint happy with your tool?

Peter


On Thu, Oct 6, 2016 at 11:08 PM, D K  wrote:

> Hi galaxy-dev,
>
> I'm having a problem running a test using planemo where I would like the
> value of a parameter taken from one of the data tables. I get the following
> error in planemo:
>
> 'Error creating a job for these tool inputs - Parameter refGenomeSource_type 
> requires a value, but has no legal values defined.\n
>
>
> From my script XML:
>
>>  
>>   
>>   
>> 
>> ...
>>   
>>   
>> 
>>  
>>   
>>
>> From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test"
> (mirrored)
>
>> 
>> value, name, path
>> 
>> 
>
>
> and from twobit.loc (where the columns are tab separated):
>
>> hsapiensH. sapiens (hg38)   /remote/RMS/users/galaxy/
>> reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
>
>
> Any suggestions would be greatly appreciated!
>
>
> ___
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>
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>
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