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!
>>
>>
>>
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
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>>
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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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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!
>>
>>
>> ___
>> 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

[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!
>
>
> ___
> 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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[galaxy-dev] planemo test with

[D K]

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!
___
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Re: [galaxy-dev] Planemo test with SGE

[D K]

Hi John,

No I haven't been able to figure this out. In answer to your questions, I
haven't modified the run.sh. I do however specify that "upload1" tool be
run on destination "local" since cluster nodes are configured such that
they can't communicate with the outside world which would prevent some of
the functionality. Is it possible that this is the problem? Could it be
that the separate parts of the test (e.g. upload, actually run a script,
set metadata, etc..), are running on different nodes and writing to
temporary locations that are not accessible to other nodes?

Thanks!

On Mon, Apr 11, 2016 at 11:08 AM, John Chilton  wrote:

> Did you ever figure this out? I cannot think of anything that would
> cause this - if the job conf is working with Galaxy it should work
> with planemo. Are you sure Galaxy was actually using the configuration
> and not just the local runner.
>
> Is it possible you've modified run.sh to modify the environment to
> change a DRMAA library path or something? I guess Pulsar would need to
> know about that same change.
>
> I did some testing this morning and added documentation to planemo
> about developing tools for clusters and testing against them and I
> didn't encounter any problems.
>
> http://planemo.readthedocs.org/en/latest/writing_advanced.html#cluster-usage
>
>
> -John
>
> On Fri, Mar 4, 2016 at 2:39 PM, D K  wrote:
> > Hi,
> >
> > I posted this question to biostars but didn't get an answer
> >
> > Is it possible to use "planemo test" functionality on an SGE cluster? I
> can
> > correctly run a custom tool on an SGE cluster when I manually run a job
> > through the galaxy interface. If I change the job_conf.xml so that the
> job
> > is run locally, I can use "planemo test" successfully, but if I change
> the
> > job_conf.xml so that Galaxy uses the SGE cluster, planemo fails:
> >
> > Traceback (most recent call last):
> >   File
> > "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py",
> line
> > 289, in test_tool
> > self.do_it( td )
> >   File
> > "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py",
> line
> > 38, in do_it
> > stage_data_in_history( galaxy_interactor, testdef.test_data(),
> > test_history, shed_tool_id )
> >   File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
> line
> > 43, in stage_data_in_history
> > upload_wait()
> >   File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
> line
> > 280, in wait
> > while not self.__history_ready( history_id ):
> >   File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
> line
> > 298, in __history_ready
> > return self._state_ready( state, error_msg="History in error state."
> )
> >   File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
> line
> > 361, in _state_ready
> > raise Exception( error_msg )
> > Exception: History in error state.
> >  >> begin captured stdout << -
> > History with id 2891970512fa2d5a in error - summary of datasets in error
> > below.
> > --
> > | 1 - MTB_Genes.fasta (HID - NAME)
> > | Dataset Blurb:
> > |  tool error
> > | Dataset Info:
> > |  The cluster DRM system terminated this job
> > | Dataset Job Standard Output:
> > |  *Standard output was empty.*
> > | Dataset Job Standard Error:
> > |  *Standard error was empty.*
> > |
> > --
> >
> > - >> end captured stdout << --
> >
> > Is this a problem with my configuration or a limitation of planemo?
> >
> >
> > Thanks!
> >
> >
> > ___
> > 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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>
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Re: [galaxy-dev] Planemo test with SGE

[John Chilton]

Did you ever figure this out? I cannot think of anything that would
cause this - if the job conf is working with Galaxy it should work
with planemo. Are you sure Galaxy was actually using the configuration
and not just the local runner.

Is it possible you've modified run.sh to modify the environment to
change a DRMAA library path or something? I guess Pulsar would need to
know about that same change.

I did some testing this morning and added documentation to planemo
about developing tools for clusters and testing against them and I
didn't encounter any problems.
http://planemo.readthedocs.org/en/latest/writing_advanced.html#cluster-usage


-John

On Fri, Mar 4, 2016 at 2:39 PM, D K  wrote:
> Hi,
>
> I posted this question to biostars but didn't get an answer
>
> Is it possible to use "planemo test" functionality on an SGE cluster? I can
> correctly run a custom tool on an SGE cluster when I manually run a job
> through the galaxy interface. If I change the job_conf.xml so that the job
> is run locally, I can use "planemo test" successfully, but if I change the
> job_conf.xml so that Galaxy uses the SGE cluster, planemo fails:
>
> Traceback (most recent call last):
>   File
> "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py", line
> 289, in test_tool
> self.do_it( td )
>   File
> "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py", line
> 38, in do_it
> stage_data_in_history( galaxy_interactor, testdef.test_data(),
> test_history, shed_tool_id )
>   File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line
> 43, in stage_data_in_history
> upload_wait()
>   File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line
> 280, in wait
> while not self.__history_ready( history_id ):
>   File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line
> 298, in __history_ready
> return self._state_ready( state, error_msg="History in error state." )
>   File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line
> 361, in _state_ready
> raise Exception( error_msg )
> Exception: History in error state.
>  >> begin captured stdout << -
> History with id 2891970512fa2d5a in error - summary of datasets in error
> below.
> --
> | 1 - MTB_Genes.fasta (HID - NAME)
> | Dataset Blurb:
> |  tool error
> | Dataset Info:
> |  The cluster DRM system terminated this job
> | Dataset Job Standard Output:
> |  *Standard output was empty.*
> | Dataset Job Standard Error:
> |  *Standard error was empty.*
> |
> --
>
> - >> end captured stdout << --
>
> Is this a problem with my configuration or a limitation of planemo?
>
>
> Thanks!
>
>
> ___
> 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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[galaxy-dev] Planemo test with SGE

[D K]

Hi,

I posted this question to biostars but didn't get an answer

Is it possible to use "planemo test" functionality on an SGE cluster? I can
correctly run a custom tool on an SGE cluster when I manually run a job
through the galaxy interface. If I change the job_conf.xml so that the job
is run locally, I can use "planemo test" successfully, but if I change the
job_conf.xml so that Galaxy uses the SGE cluster, planemo fails:

Traceback (most recent call last):
  File "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py",
line 289, in test_tool
self.do_it( td )
  File "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py",
line 38, in do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 43, in stage_data_in_history
upload_wait()
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 280, in wait
while not self.__history_ready( history_id ):
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 298, in __history_ready
return self._state_ready( state, error_msg="History in error state." )
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 361, in _state_ready
raise Exception( error_msg )
Exception: History in error state.
 >> begin captured stdout << -
History with id 2891970512fa2d5a in error - summary of datasets in error below.
--
| 1 - MTB_Genes.fasta (HID - NAME)
| Dataset Blurb:
|  tool error
| Dataset Info:
|  The cluster DRM system terminated this job
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--

- >> end captured stdout << --

Is this a problem with my configuration or a limitation of planemo?


Thanks!
___
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