Re: [galaxy-dev] TypeError with 'dict'

2014-08-15 Thread John Chilton 
Hello Martin,

You have found something of a bug - there are problems when the output
name matches an input name - in this case your conditional name
Project matches your output name Project . I think you can just
fix this by calling the output Project_output or the conditional
which_project or really anything along these lines.

I have created a Trello card to track the underlying bug -
https://trello.com/c/YDEaIlBD.

-John

On Thu, Aug 14, 2014 at 3:58 AM, Martin Christiansen
martinchristianse...@hotmail.com wrote:
 Hi again,

 Has anyone had time to look into the traceback?

 Best,
 Martin

 
 From: martinchristianse...@hotmail.com
 To: jmchil...@gmail.com; n...@bx.psu.edu
 Date: Tue, 12 Aug 2014 15:59:53 +0200

 CC: galaxy-dev@lists.bx.psu.edu
 Subject: Re: [galaxy-dev] TypeError with 'dict'

 Hi guys,

 Thanks for the response.

 I have been able to work around the from_work_dir option.
 And here are the full traceback:

 galaxy.tools ERROR 2014-08-12 15:55:35,298 Exception caught while attempting
 tool execution:
 Traceback (most recent call last):
   File /home/pcm692/galaxy-dist/lib/galaxy/tools/__init__.py, line 2004,
 in handle_single_execution
 job, out_data = self.execute( trans, incoming=params, history=history,
 rerun_remap_job_id=rerun_remap_job_id )
   File /home/pcm692/galaxy-dist/lib/galaxy/tools/__init__.py, line 2535,
 in execute
 return self.tool_action.execute( self, trans, incoming=incoming,
 set_output_hid=set_output_hid, history=history, **kwargs )
   File /home/pcm692/galaxy-dist/lib/galaxy/tools/actions/__init__.py, line
 238, in execute
 data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation
 ).get( dataid )
   File
 /home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py,
 line 767, in get
 instance = self._get_from_identity(self.session, key, False)
   File
 /home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py,
 line 2437, in _get_from_identity
 instance = session.identity_map.get(key)
   File
 /home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/identity.py,
 line 141, in get
 state = dict.get(self, key, default)
 TypeError: unhashable type: 'dict'

 Best regards,
 Martin

 Date: Tue, 12 Aug 2014 08:58:38 -0400
 From: jmchil...@gmail.com
 To: n...@bx.psu.edu
 CC: galaxy-dev@lists.bx.psu.edu
 Subject: Re: [galaxy-dev] TypeError with 'dict'

 Nate is right - full traceback would help. I am not sure it is the
 only problem - but these outputs do not look right:

 outputs
 data format=tabular name=Project label=Project

 from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
 data format=tabular name=Samples label=Samples

 from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
 /outputs

 Galaxy isn't going to expand variables ($Project.input /
 $Project.samples) in the from_work_dir attribute so those are going to
 be taken as literal strings. That directory also really needs to be
 relative to the tool directory and I believe this is enforced for
 security reasons.

 -John


 On Tue, Aug 12, 2014 at 8:55 AM, Nate Coraor n...@bx.psu.edu wrote:
  Hi Martin,
 
  If there's a full traceback instead of just this fragment, that'd
  certainly
  help with determining exactly where the problem is coming from.
 
  --nate
 
  On Aug 12, 2014, at 4:17 AM, bjoern.gruen...@googlemail.com
  bjoern.gruen...@gmail.com wrote:
 
  Hi,
 
  Galaxy stores all information about a tool and it's parameters in a
  database.
  I suppose if something is wrong with your tool, under some
  circumstances, it
  can't be stored in the database.
 
  Cheers,
  Bjoern
 
 
  2014-08-12 9:23 GMT+02:00 Martin Christiansen
  martinchristianse...@hotmail.com:
 
  Hi Björn,
 
  I'm using galaxy as a front-end to run a larger pipeline in the
  background.
  Originally I implemented the pipeline which had the same wrapper and
  was
  running fine.
  I have now begun to break it down into steps where this is the first
  step.
 
  The only thing I've changed is the output.
  How would this cause an error in the python egg?
 
  Martin
 
   Date: Tue, 12 Aug 2014 09:06:51 +0200
   From: bjoern.gruen...@gmail.com
   To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
   Subject: Re: [galaxy-dev] TypeError with 'dict'
 
  
   Hi Martin,
  
   please keep galaxy-dev in the CC list.
  
   Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
Hi Björn,
   
Most certainly. I have posted it below.
   
tool id=screen_reads name=Screen Reads
  
   - add here a version number version=0.1
  
descriptionagainst hg19/description
   
command interpreter=bashscreen_reads.sh $Project.input
$Project.samples $Project $Samples /command
   
inputs
conditional name=Project
param name=input type=select label=Select project
option value

Re: [galaxy-dev] TypeError with 'dict'

2014-08-14 Thread Martin Christiansen 
Hi again,

Has anyone had time to look into the traceback?

Best,
Martin

From: martinchristianse...@hotmail.com
To: jmchil...@gmail.com; n...@bx.psu.edu
Date: Tue, 12 Aug 2014 15:59:53 +0200
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] TypeError with 'dict'




Hi guys, 

Thanks for the response.

I have been able to work around the from_work_dir option.
And here are the full traceback:

galaxy.tools ERROR 2014-08-12 15:55:35,298 Exception caught while attempting 
tool execution:
Traceback (most recent call last):
  File /home/pcm692/galaxy-dist/lib/galaxy/tools/__init__.py, line 2004, in 
handle_single_execution
job, out_data = self.execute( trans, incoming=params, history=history, 
rerun_remap_job_id=rerun_remap_job_id )
  File /home/pcm692/galaxy-dist/lib/galaxy/tools/__init__.py, line 2535, in 
execute
return self.tool_action.execute( self, trans, incoming=incoming, 
set_output_hid=set_output_hid, history=history, **kwargs )
  File /home/pcm692/galaxy-dist/lib/galaxy/tools/actions/__init__.py, line 
238, in execute
data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation 
).get( dataid )
  File 
/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py,
 line 767, in get
instance = self._get_from_identity(self.session, key, False)
  File 
/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py,
 line 2437, in _get_from_identity
instance = session.identity_map.get(key)
  File 
/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/identity.py,
 line 141, in get
state = dict.get(self, key, default)
TypeError: unhashable type: 'dict'

Best regards, 
Martin

 Date: Tue, 12 Aug 2014 08:58:38 -0400
 From: jmchil...@gmail.com
 To: n...@bx.psu.edu
 CC: galaxy-dev@lists.bx.psu.edu
 Subject: Re: [galaxy-dev] TypeError with 'dict'
 
 Nate is right - full traceback would help. I am not sure it is the
 only problem - but these outputs do not look right:
 
 outputs
 data format=tabular name=Project label=Project
 from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
 data format=tabular name=Samples label=Samples
 from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
 /outputs
 
 Galaxy isn't going to expand variables ($Project.input /
 $Project.samples) in the from_work_dir attribute so those are going to
 be taken as literal strings. That directory also really needs to be
 relative to the tool directory and I believe this is enforced for
 security reasons.
 
 -John
 
 
 On Tue, Aug 12, 2014 at 8:55 AM, Nate Coraor n...@bx.psu.edu wrote:
  Hi Martin,
 
  If there's a full traceback instead of just this fragment, that'd certainly
  help with determining exactly where the problem is coming from.
 
  --nate
 
  On Aug 12, 2014, at 4:17 AM, bjoern.gruen...@googlemail.com
  bjoern.gruen...@gmail.com wrote:
 
  Hi,
 
  Galaxy stores all information about a tool and it's parameters in a
  database.
  I suppose if something is wrong with your tool, under some circumstances, it
  can't be stored in the database.
 
  Cheers,
  Bjoern
 
 
  2014-08-12 9:23 GMT+02:00 Martin Christiansen
  martinchristianse...@hotmail.com:
 
  Hi Björn,
 
  I'm using galaxy as a front-end to run a larger pipeline in the
  background.
  Originally I implemented the pipeline which had the same wrapper and was
  running fine.
  I have now begun to break it down into steps where this is the first step.
 
  The only thing I've changed is the output.
  How would this cause an error in the python egg?
 
  Martin
 
   Date: Tue, 12 Aug 2014 09:06:51 +0200
   From: bjoern.gruen...@gmail.com
   To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
   Subject: Re: [galaxy-dev] TypeError with 'dict'
 
  
   Hi Martin,
  
   please keep galaxy-dev in the CC list.
  
   Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
Hi Björn,
   
Most certainly. I have posted it below.
   
tool id=screen_reads name=Screen Reads
  
   - add here a version number version=0.1
  
descriptionagainst hg19/description
   
command interpreter=bashscreen_reads.sh $Project.input
$Project.samples $Project $Samples /command
   
inputs
conditional name=Project
param name=input type=select label=Select project
option value=galaxy_test1galaxy_test1/option
option value=Untitled FolderUntitled Folder/option
  
   - is the white space really needed? If so $Project.input will be two
   words. Use ${Project.input} to convert it to onw argument
  
/param
when value=galaxy_test1
param name=samples type=select label=Select samples
display=checkboxes multiple=True
option value=147406386-700171390147406386-700171390/option
option value=158256496-700097688158256496-700097688/option
option value=158337416-700013715158337416-700013715/option
option value=158337416

Re: [galaxy-dev] TypeError with 'dict'

2014-08-12 Thread Björn Grüning 

Hi Martin,

please keep galaxy-dev in the CC list.

Am 12.08.2014 um 08:51 schrieb Martin Christiansen:

Hi Björn,

Most certainly. I have posted it below.

tool id=screen_reads name=Screen Reads


- add here a version number version=0.1


descriptionagainst hg19/description

command interpreter=bashscreen_reads.sh $Project.input $Project.samples $Project 
$Samples /command

inputs
 conditional name=Project
 param name=input type=select label=Select project
 option value=galaxy_test1galaxy_test1/option
 option value=Untitled FolderUntitled Folder/option


- is the white space really needed? If so $Project.input will be two 
words. Use ${Project.input} to convert it to onw argument



 /param
 when value=galaxy_test1
 param name=samples type=select label=Select samples display=checkboxes 
multiple=True
 option 
value=147406386-700171390147406386-700171390/option
 option 
value=158256496-700097688158256496-700097688/option
 option 
value=158337416-700013715158337416-700013715/option
 option 
value=158337416-700097837158337416-700097837/option
 option 
value=158357646-700035237158357646-700035237/option
 option 
value=158458797-700014562158458797-700014562/option
 option 
value=158479027-700014724158479027-700014724/option
 option 
value=158479027-700097196158479027-700097196/option
 option 
value=158499257-700014837158499257-700014837/option
 option 
value=158499257-700098561158499257-700098561/option
 option 
value=158742018-700015181158742018-700015181/option
 option 
value=158802708-700015245158802708-700015245/option
 option 
value=158802708-700015250158802708-700015250/option
 option 
value=158802708-700099803158802708-700099803/option
 option 
value=158802708-700119165158802708-700119165/option
 option 
value=158822939-700014954158822939-700014954/option
 option 
value=158883629-700015113158883629-700015113/option
 option 
value=158883629-700100227158883629-700100227/option
 option 
value=158883629-700112812158883629-700112812/option
 option 
value=158924089-700099307158924089-700099307/option
 /param
 /when
 when value=Untitled Folder
 param name=samples type=select label=Select samples display=checkboxes 
multiple=True


- you don't have any option here.


 /param
 /when
 /conditional
/inputs

outputs
 data format=tabular name=Project label=Project 
from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
 data format=tabular name=Samples label=Samples 
from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
/outputs


- I'm not sure this will work. workdir is a special dir Galaxy creates 
for you. It will be the working directory where your program get's 
called. So assume your program creates foo.sam files. You can specify it 
like from_work_dir='foo.sam'


The input handling looks also a little bit strange. You do not specify 
any input file in Galaxy. That is not really Galaxy like :)


Cheers,
Bjoern


help
Reads screened against hg19.
/help
/tool

Best,
Martin



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Re: [galaxy-dev] TypeError with 'dict'

2014-08-12 Thread Martin Christiansen 
Hi Björn, 

It looks like this.

tool id=screen_reads name=Screen Reads

descriptionagainst hg19/description

command interpreter=bashscreen_reads.sh $Project.input $Project.samples 
$Project $Samples /command

inputs
conditional name=Project
param name=input type=select label=Select project
option value=galaxy_test1galaxy_test1/option
option value=Untitled FolderUntitled Folder/option
/param
when value=galaxy_test1
param name=samples type=select label=Select samples 
display=checkboxes multiple=True
option value=147406386-700171390147406386-700171390/option
option value=158256496-700097688158256496-700097688/option
option value=158337416-700013715158337416-700013715/option
option value=158337416-700097837158337416-700097837/option
option value=158357646-700035237158357646-700035237/option
option value=158458797-700014562158458797-700014562/option
option value=158479027-700014724158479027-700014724/option
option value=158479027-700097196158479027-700097196/option
option value=158499257-700014837158499257-700014837/option
option value=158499257-700098561158499257-700098561/option
option value=158742018-700015181158742018-700015181/option
option value=158802708-700015245158802708-700015245/option
option value=158802708-700015250158802708-700015250/option
option value=158802708-700099803158802708-700099803/option
option value=158802708-700119165158802708-700119165/option
option value=158822939-700014954158822939-700014954/option
option value=158883629-700015113158883629-700015113/option
option value=158883629-700100227158883629-700100227/option
option value=158883629-700112812158883629-700112812/option
option value=158924089-700099307158924089-700099307/option
/param
/when
when value=Untitled Folder
param name=samples type=select label=Select samples 
display=checkboxes multiple=True
/param
/when
/conditional
/inputs

outputs
data format=tabular name=Project label=Project 
from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
data format=tabular name=Samples label=Samples 
from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
/outputs

help
Reads screened against hg19.
/help
/tool

Best,
Martin
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Please keep all replies on the list by using reply all
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Re: [galaxy-dev] TypeError with 'dict'

2014-08-12 Thread Martin Christiansen 
Hi Björn,

I'm using galaxy as a front-end to run a larger pipeline in the background.
Originally I implemented the pipeline which had the same wrapper and was 
running fine. 
I have now begun to break it down into steps where this is the first step.

The only thing I've changed is the output.
How would this cause an error in the python egg?

Martin

 Date: Tue, 12 Aug 2014 09:06:51 +0200
 From: bjoern.gruen...@gmail.com
 To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
 Subject: Re: [galaxy-dev] TypeError with 'dict'
 
 Hi Martin,
 
 please keep galaxy-dev in the CC list.
 
 Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
  Hi Björn,
 
  Most certainly. I have posted it below.
 
  tool id=screen_reads name=Screen Reads
 
 - add here a version number version=0.1
 
  descriptionagainst hg19/description
 
  command interpreter=bashscreen_reads.sh $Project.input $Project.samples 
  $Project $Samples /command
 
  inputs
   conditional name=Project
   param name=input type=select label=Select project
   option value=galaxy_test1galaxy_test1/option
   option value=Untitled FolderUntitled Folder/option
 
 - is the white space really needed? If so $Project.input will be two 
 words. Use ${Project.input} to convert it to onw argument
 
   /param
   when value=galaxy_test1
   param name=samples type=select label=Select samples 
  display=checkboxes multiple=True
   option 
  value=147406386-700171390147406386-700171390/option
   option 
  value=158256496-700097688158256496-700097688/option
   option 
  value=158337416-700013715158337416-700013715/option
   option 
  value=158337416-700097837158337416-700097837/option
   option 
  value=158357646-700035237158357646-700035237/option
   option 
  value=158458797-700014562158458797-700014562/option
   option 
  value=158479027-700014724158479027-700014724/option
   option 
  value=158479027-700097196158479027-700097196/option
   option 
  value=158499257-700014837158499257-700014837/option
   option 
  value=158499257-700098561158499257-700098561/option
   option 
  value=158742018-700015181158742018-700015181/option
   option 
  value=158802708-700015245158802708-700015245/option
   option 
  value=158802708-700015250158802708-700015250/option
   option 
  value=158802708-700099803158802708-700099803/option
   option 
  value=158802708-700119165158802708-700119165/option
   option 
  value=158822939-700014954158822939-700014954/option
   option 
  value=158883629-700015113158883629-700015113/option
   option 
  value=158883629-700100227158883629-700100227/option
   option 
  value=158883629-700112812158883629-700112812/option
   option 
  value=158924089-700099307158924089-700099307/option
   /param
   /when
   when value=Untitled Folder
   param name=samples type=select label=Select samples 
  display=checkboxes multiple=True
 
 - you don't have any option here.
 
   /param
   /when
   /conditional
  /inputs
 
  outputs
   data format=tabular name=Project label=Project 
  from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
   data format=tabular name=Samples label=Samples 
  from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
  /outputs
 
 - I'm not sure this will work. workdir is a special dir Galaxy creates 
 for you. It will be the working directory where your program get's 
 called. So assume your program creates foo.sam files. You can specify it 
 like from_work_dir='foo.sam'
 
 The input handling looks also a little bit strange. You do not specify 
 any input file in Galaxy. That is not really Galaxy like :)
 
 Cheers,
 Bjoern
 
  help
  Reads screened against hg19.
  /help
  /tool
 
  Best,
  Martin
  
 
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Please keep all replies on the list by using reply all
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Re: [galaxy-dev] TypeError with 'dict'

2014-08-12 Thread bjoern.gruen...@googlemail.com 
Hi,

Galaxy stores all information about a tool and it's parameters in a
database.
I suppose if something is wrong with your tool, under some circumstances,
it can't be stored in the database.

Cheers,
Bjoern


2014-08-12 9:23 GMT+02:00 Martin Christiansen 
martinchristianse...@hotmail.com:

 Hi Björn,

 I'm using galaxy as a front-end to run a larger pipeline in the background.
 Originally I implemented the pipeline which had the same wrapper and was
 running fine.
 I have now begun to break it down into steps where this is the first step.

 The only thing I've changed is the output.
 How would this cause an error in the python egg?

 Martin

  Date: Tue, 12 Aug 2014 09:06:51 +0200
  From: bjoern.gruen...@gmail.com
  To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
  Subject: Re: [galaxy-dev] TypeError with 'dict'

 
  Hi Martin,
 
  please keep galaxy-dev in the CC list.
 
  Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
   Hi Björn,
  
   Most certainly. I have posted it below.
  
   tool id=screen_reads name=Screen Reads
 
  - add here a version number version=0.1
 
   descriptionagainst hg19/description
  
   command interpreter=bashscreen_reads.sh $Project.input
 $Project.samples $Project $Samples /command
  
   inputs
   conditional name=Project
   param name=input type=select label=Select project
   option value=galaxy_test1galaxy_test1/option
   option value=Untitled FolderUntitled Folder/option
 
  - is the white space really needed? If so $Project.input will be two
  words. Use ${Project.input} to convert it to onw argument
 
   /param
   when value=galaxy_test1
   param name=samples type=select label=Select samples
 display=checkboxes multiple=True
   option value=147406386-700171390147406386-700171390/option
   option value=158256496-700097688158256496-700097688/option
   option value=158337416-700013715158337416-700013715/option
   option value=158337416-700097837158337416-700097837/option
   option value=158357646-700035237158357646-700035237/option
   option value=158458797-700014562158458797-700014562/option
   option value=158479027-700014724158479027-700014724/option
   option value=158479027-700097196158479027-700097196/option
   option value=158499257-700014837158499257-700014837/option
   option value=158499257-700098561158499257-700098561/option
   option value=158742018-700015181158742018-700015181/option
   option value=158802708-700015245158802708-700015245/option
   option value=158802708-700015250158802708-700015250/option
   option value=158802708-700099803158802708-700099803/option
   option value=158802708-700119165158802708-700119165/option
   option value=158822939-700014954158822939-700014954/option
   option value=158883629-700015113158883629-700015113/option
   option value=158883629-700100227158883629-700100227/option
   option value=158883629-700112812158883629-700112812/option
   option value=158924089-700099307158924089-700099307/option
   /param
   /when
   when value=Untitled Folder
   param name=samples type=select label=Select samples
 display=checkboxes multiple=True
 
  - you don't have any option here.
 
   /param
   /when
   /conditional
   /inputs
  
   outputs
   data format=tabular name=Project label=Project
 from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
   data format=tabular name=Samples label=Samples
 from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
   /outputs
 
  - I'm not sure this will work. workdir is a special dir Galaxy creates
  for you. It will be the working directory where your program get's
  called. So assume your program creates foo.sam files. You can specify it
  like from_work_dir='foo.sam'
 
  The input handling looks also a little bit strange. You do not specify
  any input file in Galaxy. That is not really Galaxy like :)
 
  Cheers,
  Bjoern
 
   help
   Reads screened against hg19.
   /help
   /tool
  
   Best,
   Martin
  
  

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Re: [galaxy-dev] TypeError with 'dict'

2014-08-12 Thread Nate Coraor 
Hi Martin,

If there's a full traceback instead of just this fragment, that'd certainly 
help with determining exactly where the problem is coming from.

--nate

On Aug 12, 2014, at 4:17 AM, bjoern.gruen...@googlemail.com 
bjoern.gruen...@gmail.com wrote:

 Hi,
 
 Galaxy stores all information about a tool and it's parameters in a database. 
 I suppose if something is wrong with your tool, under some circumstances, it 
 can't be stored in the database.
 
 Cheers,
 Bjoern
 
 
 2014-08-12 9:23 GMT+02:00 Martin Christiansen 
 martinchristianse...@hotmail.com:
 Hi Björn,
 
 I'm using galaxy as a front-end to run a larger pipeline in the background.
 Originally I implemented the pipeline which had the same wrapper and was 
 running fine. 
 I have now begun to break it down into steps where this is the first step.
 
 The only thing I've changed is the output.
 How would this cause an error in the python egg?
 
 Martin
 
  Date: Tue, 12 Aug 2014 09:06:51 +0200
  From: bjoern.gruen...@gmail.com
  To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
  Subject: Re: [galaxy-dev] TypeError with 'dict'
 
  
  Hi Martin,
  
  please keep galaxy-dev in the CC list.
  
  Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
   Hi Björn,
  
   Most certainly. I have posted it below.
  
   tool id=screen_reads name=Screen Reads
  
  - add here a version number version=0.1
  
   descriptionagainst hg19/description
  
   command interpreter=bashscreen_reads.sh $Project.input 
   $Project.samples $Project $Samples /command
  
   inputs
   conditional name=Project
   param name=input type=select label=Select project
   option value=galaxy_test1galaxy_test1/option
   option value=Untitled FolderUntitled Folder/option
  
  - is the white space really needed? If so $Project.input will be two 
  words. Use ${Project.input} to convert it to onw argument
  
   /param
   when value=galaxy_test1
   param name=samples type=select label=Select samples 
   display=checkboxes multiple=True
   option value=147406386-700171390147406386-700171390/option
   option value=158256496-700097688158256496-700097688/option
   option value=158337416-700013715158337416-700013715/option
   option value=158337416-700097837158337416-700097837/option
   option value=158357646-700035237158357646-700035237/option
   option value=158458797-700014562158458797-700014562/option
   option value=158479027-700014724158479027-700014724/option
   option value=158479027-700097196158479027-700097196/option
   option value=158499257-700014837158499257-700014837/option
   option value=158499257-700098561158499257-700098561/option
   option value=158742018-700015181158742018-700015181/option
   option value=158802708-700015245158802708-700015245/option
   option value=158802708-700015250158802708-700015250/option
   option value=158802708-700099803158802708-700099803/option
   option value=158802708-700119165158802708-700119165/option
   option value=158822939-700014954158822939-700014954/option
   option value=158883629-700015113158883629-700015113/option
   option value=158883629-700100227158883629-700100227/option
   option value=158883629-700112812158883629-700112812/option
   option value=158924089-700099307158924089-700099307/option
   /param
   /when
   when value=Untitled Folder
   param name=samples type=select label=Select samples 
   display=checkboxes multiple=True
  
  - you don't have any option here.
  
   /param
   /when
   /conditional
   /inputs
  
   outputs
   data format=tabular name=Project label=Project 
   from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
   data format=tabular name=Samples label=Samples 
   from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
   /outputs
  
  - I'm not sure this will work. workdir is a special dir Galaxy creates 
  for you. It will be the working directory where your program get's 
  called. So assume your program creates foo.sam files. You can specify it 
  like from_work_dir='foo.sam'
  
  The input handling looks also a little bit strange. You do not specify 
  any input file in Galaxy. That is not really Galaxy like :)
  
  Cheers,
  Bjoern
  
   help
   Reads screened against hg19.
   /help
   /tool
  
   Best,
   Martin
   
  
 
 ___
 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:
  http://lists.bx.psu.edu/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

___
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search

Re: [galaxy-dev] TypeError with 'dict'

2014-08-12 Thread John Chilton 
Nate is right - full traceback would help. I am not sure it is the
only problem - but these outputs do not look right:

outputs
data format=tabular name=Project label=Project
from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
data format=tabular name=Samples label=Samples
from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
/outputs

Galaxy isn't going to expand variables ($Project.input /
$Project.samples) in the from_work_dir attribute so those are going to
be taken as literal strings. That directory also really needs to be
relative to the tool directory and I believe this is enforced for
security reasons.

-John


On Tue, Aug 12, 2014 at 8:55 AM, Nate Coraor n...@bx.psu.edu wrote:
 Hi Martin,

 If there's a full traceback instead of just this fragment, that'd certainly
 help with determining exactly where the problem is coming from.

 --nate

 On Aug 12, 2014, at 4:17 AM, bjoern.gruen...@googlemail.com
 bjoern.gruen...@gmail.com wrote:

 Hi,

 Galaxy stores all information about a tool and it's parameters in a
 database.
 I suppose if something is wrong with your tool, under some circumstances, it
 can't be stored in the database.

 Cheers,
 Bjoern


 2014-08-12 9:23 GMT+02:00 Martin Christiansen
 martinchristianse...@hotmail.com:

 Hi Björn,

 I'm using galaxy as a front-end to run a larger pipeline in the
 background.
 Originally I implemented the pipeline which had the same wrapper and was
 running fine.
 I have now begun to break it down into steps where this is the first step.

 The only thing I've changed is the output.
 How would this cause an error in the python egg?

 Martin

  Date: Tue, 12 Aug 2014 09:06:51 +0200
  From: bjoern.gruen...@gmail.com
  To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
  Subject: Re: [galaxy-dev] TypeError with 'dict'

 
  Hi Martin,
 
  please keep galaxy-dev in the CC list.
 
  Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
   Hi Björn,
  
   Most certainly. I have posted it below.
  
   tool id=screen_reads name=Screen Reads
 
  - add here a version number version=0.1
 
   descriptionagainst hg19/description
  
   command interpreter=bashscreen_reads.sh $Project.input
   $Project.samples $Project $Samples /command
  
   inputs
   conditional name=Project
   param name=input type=select label=Select project
   option value=galaxy_test1galaxy_test1/option
   option value=Untitled FolderUntitled Folder/option
 
  - is the white space really needed? If so $Project.input will be two
  words. Use ${Project.input} to convert it to onw argument
 
   /param
   when value=galaxy_test1
   param name=samples type=select label=Select samples
   display=checkboxes multiple=True
   option value=147406386-700171390147406386-700171390/option
   option value=158256496-700097688158256496-700097688/option
   option value=158337416-700013715158337416-700013715/option
   option value=158337416-700097837158337416-700097837/option
   option value=158357646-700035237158357646-700035237/option
   option value=158458797-700014562158458797-700014562/option
   option value=158479027-700014724158479027-700014724/option
   option value=158479027-700097196158479027-700097196/option
   option value=158499257-700014837158499257-700014837/option
   option value=158499257-700098561158499257-700098561/option
   option value=158742018-700015181158742018-700015181/option
   option value=158802708-700015245158802708-700015245/option
   option value=158802708-700015250158802708-700015250/option
   option value=158802708-700099803158802708-700099803/option
   option value=158802708-700119165158802708-700119165/option
   option value=158822939-700014954158822939-700014954/option
   option value=158883629-700015113158883629-700015113/option
   option value=158883629-700100227158883629-700100227/option
   option value=158883629-700112812158883629-700112812/option
   option value=158924089-700099307158924089-700099307/option
   /param
   /when
   when value=Untitled Folder
   param name=samples type=select label=Select samples
   display=checkboxes multiple=True
 
  - you don't have any option here.
 
   /param
   /when
   /conditional
   /inputs
  
   outputs
   data format=tabular name=Project label=Project
   from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
   data format=tabular name=Samples label=Samples
   from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
   /outputs
 
  - I'm not sure this will work. workdir is a special dir Galaxy creates
  for you. It will be the working directory where your program get's
  called. So assume your program creates foo.sam files. You can specify it
  like from_work_dir='foo.sam'
 
  The input handling looks also a little bit strange. You do not specify
  any input file in Galaxy. That is not really Galaxy like :)
 
  Cheers,
  Bjoern
 
   help
   Reads screened against hg19.
   /help
   /tool
  
   Best

Re: [galaxy-dev] TypeError with 'dict'

2014-08-12 Thread Martin Christiansen 
Hi guys, 

Thanks for the response.

I have been able to work around the from_work_dir option.
And here are the full traceback:

galaxy.tools ERROR 2014-08-12 15:55:35,298 Exception caught while attempting 
tool execution:
Traceback (most recent call last):
  File /home/pcm692/galaxy-dist/lib/galaxy/tools/__init__.py, line 2004, in 
handle_single_execution
job, out_data = self.execute( trans, incoming=params, history=history, 
rerun_remap_job_id=rerun_remap_job_id )
  File /home/pcm692/galaxy-dist/lib/galaxy/tools/__init__.py, line 2535, in 
execute
return self.tool_action.execute( self, trans, incoming=incoming, 
set_output_hid=set_output_hid, history=history, **kwargs )
  File /home/pcm692/galaxy-dist/lib/galaxy/tools/actions/__init__.py, line 
238, in execute
data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation 
).get( dataid )
  File 
/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py,
 line 767, in get
instance = self._get_from_identity(self.session, key, False)
  File 
/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py,
 line 2437, in _get_from_identity
instance = session.identity_map.get(key)
  File 
/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/identity.py,
 line 141, in get
state = dict.get(self, key, default)
TypeError: unhashable type: 'dict'

Best regards, 
Martin

 Date: Tue, 12 Aug 2014 08:58:38 -0400
 From: jmchil...@gmail.com
 To: n...@bx.psu.edu
 CC: galaxy-dev@lists.bx.psu.edu
 Subject: Re: [galaxy-dev] TypeError with 'dict'
 
 Nate is right - full traceback would help. I am not sure it is the
 only problem - but these outputs do not look right:
 
 outputs
 data format=tabular name=Project label=Project
 from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
 data format=tabular name=Samples label=Samples
 from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
 /outputs
 
 Galaxy isn't going to expand variables ($Project.input /
 $Project.samples) in the from_work_dir attribute so those are going to
 be taken as literal strings. That directory also really needs to be
 relative to the tool directory and I believe this is enforced for
 security reasons.
 
 -John
 
 
 On Tue, Aug 12, 2014 at 8:55 AM, Nate Coraor n...@bx.psu.edu wrote:
  Hi Martin,
 
  If there's a full traceback instead of just this fragment, that'd certainly
  help with determining exactly where the problem is coming from.
 
  --nate
 
  On Aug 12, 2014, at 4:17 AM, bjoern.gruen...@googlemail.com
  bjoern.gruen...@gmail.com wrote:
 
  Hi,
 
  Galaxy stores all information about a tool and it's parameters in a
  database.
  I suppose if something is wrong with your tool, under some circumstances, it
  can't be stored in the database.
 
  Cheers,
  Bjoern
 
 
  2014-08-12 9:23 GMT+02:00 Martin Christiansen
  martinchristianse...@hotmail.com:
 
  Hi Björn,
 
  I'm using galaxy as a front-end to run a larger pipeline in the
  background.
  Originally I implemented the pipeline which had the same wrapper and was
  running fine.
  I have now begun to break it down into steps where this is the first step.
 
  The only thing I've changed is the output.
  How would this cause an error in the python egg?
 
  Martin
 
   Date: Tue, 12 Aug 2014 09:06:51 +0200
   From: bjoern.gruen...@gmail.com
   To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
   Subject: Re: [galaxy-dev] TypeError with 'dict'
 
  
   Hi Martin,
  
   please keep galaxy-dev in the CC list.
  
   Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
Hi Björn,
   
Most certainly. I have posted it below.
   
tool id=screen_reads name=Screen Reads
  
   - add here a version number version=0.1
  
descriptionagainst hg19/description
   
command interpreter=bashscreen_reads.sh $Project.input
$Project.samples $Project $Samples /command
   
inputs
conditional name=Project
param name=input type=select label=Select project
option value=galaxy_test1galaxy_test1/option
option value=Untitled FolderUntitled Folder/option
  
   - is the white space really needed? If so $Project.input will be two
   words. Use ${Project.input} to convert it to onw argument
  
/param
when value=galaxy_test1
param name=samples type=select label=Select samples
display=checkboxes multiple=True
option value=147406386-700171390147406386-700171390/option
option value=158256496-700097688158256496-700097688/option
option value=158337416-700013715158337416-700013715/option
option value=158337416-700097837158337416-700097837/option
option value=158357646-700035237158357646-700035237/option
option value=158458797-700014562158458797-700014562/option
option value=158479027-700014724158479027-700014724/option
option value=158479027-700097196158479027-700097196