TypeError with 'dict'

classic Classic list List threaded Threaded
11 messages Options
Reply | Threaded
Open this post in threaded view
|

TypeError with 'dict'

Martin Christiansen
Hi all,

I'm setting up a local galaxy server and have implemented a tool, but I can't even get it to run.
When I try to run it, the terminal says:
TypeError: unhashable type: 'dict'

The error itself arises from a python egg:
File "~/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)

Any suggestions of how to solve this?

Best regards,
Martin Christiansen

___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: TypeError with 'dict'

Björn Grüning-3
Hi Martin,

can you show us the code of your tool wrapper?

Thanks,
Bjoern

Am 12.08.2014 um 08:43 schrieb Martin Christiansen:

> Hi all,
>
> I'm setting up a local galaxy server and have implemented a tool, but I can't even get it to run.
> When I try to run it, the terminal says:
> TypeError: unhashable type: 'dict'
>
> The error itself arises from a python egg:
> File "~/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)
>
> Any suggestions of how to solve this?
>
> Best regards,
> Martin Christiansen
>
>
>    
>
>
>
> ___________________________________________________________
> 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/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: TypeError with 'dict'

Björn Grüning-3
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"

> <description>against hg19</description>
>
> <command interpreter="bash">screen_reads.sh $Project.input $Project.samples $Project $Samples </command>
>
> <inputs>
>      <conditional name="Project">
>          <param name="input" type="select" label="Select project">
>              <option value="galaxy_test1">galaxy_test1</option>
>              <option value="Untitled Folder">Untitled 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="147406386-700171390">147406386-700171390</option>
>                  <option value="158256496-700097688">158256496-700097688</option>
>                  <option value="158337416-700013715">158337416-700013715</option>
>                  <option value="158337416-700097837">158337416-700097837</option>
>                  <option value="158357646-700035237">158357646-700035237</option>
>                  <option value="158458797-700014562">158458797-700014562</option>
>                  <option value="158479027-700014724">158479027-700014724</option>
>                  <option value="158479027-700097196">158479027-700097196</option>
>                  <option value="158499257-700014837">158499257-700014837</option>
>                  <option value="158499257-700098561">158499257-700098561</option>
>                  <option value="158742018-700015181">158742018-700015181</option>
>                  <option value="158802708-700015245">158802708-700015245</option>
>                  <option value="158802708-700015250">158802708-700015250</option>
>                  <option value="158802708-700099803">158802708-700099803</option>
>                  <option value="158802708-700119165">158802708-700119165</option>
>                  <option value="158822939-700014954">158822939-700014954</option>
>                  <option value="158883629-700015113">158883629-700015113</option>
>                  <option value="158883629-700100227">158883629-700100227</option>
>                  <option value="158883629-700112812">158883629-700112812</option>
>                  <option value="158924089-700099307">158924089-700099307</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/
Reply | Threaded
Open this post in threaded view
|

Re: TypeError with 'dict'

Martin Christiansen
In reply to this post by Björn Grüning-3
Hi Björn,

It looks like this.

<tool id="screen_reads" name="Screen Reads">

<description>against hg19</description>

<command interpreter="bash">screen_reads.sh $Project.input $Project.samples $Project $Samples </command>

<inputs>
    <conditional name="Project">
        <param name="input" type="select" label="Select project">
            <option value="galaxy_test1">galaxy_test1</option>
            <option value="Untitled Folder">Untitled Folder</option>
        </param>
        <when value="galaxy_test1">
            <param name="samples" type="select" label="Select samples" display="checkboxes" multiple="True">
                <option value="147406386-700171390">147406386-700171390</option>
                <option value="158256496-700097688">158256496-700097688</option>
                <option value="158337416-700013715">158337416-700013715</option>
                <option value="158337416-700097837">158337416-700097837</option>
                <option value="158357646-700035237">158357646-700035237</option>
                <option value="158458797-700014562">158458797-700014562</option>
                <option value="158479027-700014724">158479027-700014724</option>
                <option value="158479027-700097196">158479027-700097196</option>
                <option value="158499257-700014837">158499257-700014837</option>
                <option value="158499257-700098561">158499257-700098561</option>
                <option value="158742018-700015181">158742018-700015181</option>
                <option value="158802708-700015245">158802708-700015245</option>
                <option value="158802708-700015250">158802708-700015250</option>
                <option value="158802708-700099803">158802708-700099803</option>
                <option value="158802708-700119165">158802708-700119165</option>
                <option value="158822939-700014954">158822939-700014954</option>
                <option value="158883629-700015113">158883629-700015113</option>
                <option value="158883629-700100227">158883629-700100227</option>
                <option value="158883629-700112812">158883629-700112812</option>
                <option value="158924089-700099307">158924089-700099307</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

___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: TypeError with 'dict'

Martin Christiansen
In reply to this post by Björn Grüning-3
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: [hidden email]
> To: [hidden email]; [hidden email]
> 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"
>
> > <description>against hg19</description>
> >
> > <command interpreter="bash">screen_reads.sh $Project.input $Project.samples $Project $Samples </command>
> >
> > <inputs>
> > <conditional name="Project">
> > <param name="input" type="select" label="Select project">
> > <option value="galaxy_test1">galaxy_test1</option>
> > <option value="Untitled Folder">Untitled 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="147406386-700171390">147406386-700171390</option>
> > <option value="158256496-700097688">158256496-700097688</option>
> > <option value="158337416-700013715">158337416-700013715</option>
> > <option value="158337416-700097837">158337416-700097837</option>
> > <option value="158357646-700035237">158357646-700035237</option>
> > <option value="158458797-700014562">158458797-700014562</option>
> > <option value="158479027-700014724">158479027-700014724</option>
> > <option value="158479027-700097196">158479027-700097196</option>
> > <option value="158499257-700014837">158499257-700014837</option>
> > <option value="158499257-700098561">158499257-700098561</option>
> > <option value="158742018-700015181">158742018-700015181</option>
> > <option value="158802708-700015245">158802708-700015245</option>
> > <option value="158802708-700015250">158802708-700015250</option>
> > <option value="158802708-700099803">158802708-700099803</option>
> > <option value="158802708-700119165">158802708-700119165</option>
> > <option value="158822939-700014954">158822939-700014954</option>
> > <option value="158883629-700015113">158883629-700015113</option>
> > <option value="158883629-700100227">158883629-700100227</option>
> > <option value="158883629-700112812">158883629-700112812</option>
> > <option value="158924089-700099307">158924089-700099307</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/
Reply | Threaded
Open this post in threaded view
|

Re: TypeError with 'dict'

Björn Grüning-3
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 <[hidden email]>:
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: [hidden email]
> To: [hidden email]; [hidden email]

> 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"
>
> > <description>against hg19</description>
> >
> > <command interpreter="bash">screen_reads.sh $Project.input $Project.samples $Project $Samples </command>
> >
> > <inputs>
> > <conditional name="Project">
> > <param name="input" type="select" label="Select project">
> > <option value="galaxy_test1">galaxy_test1</option>
> > <option value="Untitled Folder">Untitled 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="147406386-700171390">147406386-700171390</option>
> > <option value="158256496-700097688">158256496-700097688</option>
> > <option value="158337416-700013715">158337416-700013715</option>
> > <option value="158337416-700097837">158337416-700097837</option>
> > <option value="158357646-700035237">158357646-700035237</option>
> > <option value="158458797-700014562">158458797-700014562</option>
> > <option value="158479027-700014724">158479027-700014724</option>
> > <option value="158479027-700097196">158479027-700097196</option>
> > <option value="158499257-700014837">158499257-700014837</option>
> > <option value="158499257-700098561">158499257-700098561</option>
> > <option value="158742018-700015181">158742018-700015181</option>
> > <option value="158802708-700015245">158802708-700015245</option>
> > <option value="158802708-700015250">158802708-700015250</option>
> > <option value="158802708-700099803">158802708-700099803</option>
> > <option value="158802708-700119165">158802708-700119165</option>
> > <option value="158822939-700014954">158822939-700014954</option>
> > <option value="158883629-700015113">158883629-700015113</option>
> > <option value="158883629-700100227">158883629-700100227</option>
> > <option value="158883629-700112812">158883629-700112812</option>
> > <option value="158924089-700099307">158924089-700099307</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/
Reply | Threaded
Open this post in threaded view
|

Re: TypeError with 'dict'

Nate Coraor (nate@bx.psu.edu)
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, [hidden email] <[hidden email]> 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 <[hidden email]>:
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: [hidden email]
> To: [hidden email]; [hidden email]

> 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"
>
> > <description>against hg19</description>
> >
> > <command interpreter="bash">screen_reads.sh $Project.input $Project.samples $Project $Samples </command>
> >
> > <inputs>
> > <conditional name="Project">
> > <param name="input" type="select" label="Select project">
> > <option value="galaxy_test1">galaxy_test1</option>
> > <option value="Untitled Folder">Untitled 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="147406386-700171390">147406386-700171390</option>
> > <option value="158256496-700097688">158256496-700097688</option>
> > <option value="158337416-700013715">158337416-700013715</option>
> > <option value="158337416-700097837">158337416-700097837</option>
> > <option value="158357646-700035237">158357646-700035237</option>
> > <option value="158458797-700014562">158458797-700014562</option>
> > <option value="158479027-700014724">158479027-700014724</option>
> > <option value="158479027-700097196">158479027-700097196</option>
> > <option value="158499257-700014837">158499257-700014837</option>
> > <option value="158499257-700098561">158499257-700098561</option>
> > <option value="158742018-700015181">158742018-700015181</option>
> > <option value="158802708-700015245">158802708-700015245</option>
> > <option value="158802708-700015250">158802708-700015250</option>
> > <option value="158802708-700099803">158802708-700099803</option>
> > <option value="158802708-700119165">158802708-700119165</option>
> > <option value="158822939-700014954">158822939-700014954</option>
> > <option value="158883629-700015113">158883629-700015113</option>
> > <option value="158883629-700100227">158883629-700100227</option>
> > <option value="158883629-700112812">158883629-700112812</option>
> > <option value="158924089-700099307">158924089-700099307</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/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: TypeError with 'dict'

John Chilton-4
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 <[hidden email]> 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, [hidden email]
> <[hidden email]> 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
> <[hidden email]>:
>>
>> 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: [hidden email]
>> > To: [hidden email]; [hidden email]
>> > 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"
>> >
>> > > <description>against hg19</description>
>> > >
>> > > <command interpreter="bash">screen_reads.sh $Project.input
>> > > $Project.samples $Project $Samples </command>
>> > >
>> > > <inputs>
>> > > <conditional name="Project">
>> > > <param name="input" type="select" label="Select project">
>> > > <option value="galaxy_test1">galaxy_test1</option>
>> > > <option value="Untitled Folder">Untitled 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="147406386-700171390">147406386-700171390</option>
>> > > <option value="158256496-700097688">158256496-700097688</option>
>> > > <option value="158337416-700013715">158337416-700013715</option>
>> > > <option value="158337416-700097837">158337416-700097837</option>
>> > > <option value="158357646-700035237">158357646-700035237</option>
>> > > <option value="158458797-700014562">158458797-700014562</option>
>> > > <option value="158479027-700014724">158479027-700014724</option>
>> > > <option value="158479027-700097196">158479027-700097196</option>
>> > > <option value="158499257-700014837">158499257-700014837</option>
>> > > <option value="158499257-700098561">158499257-700098561</option>
>> > > <option value="158742018-700015181">158742018-700015181</option>
>> > > <option value="158802708-700015245">158802708-700015245</option>
>> > > <option value="158802708-700015250">158802708-700015250</option>
>> > > <option value="158802708-700099803">158802708-700099803</option>
>> > > <option value="158802708-700119165">158802708-700119165</option>
>> > > <option value="158822939-700014954">158822939-700014954</option>
>> > > <option value="158883629-700015113">158883629-700015113</option>
>> > > <option value="158883629-700100227">158883629-700100227</option>
>> > > <option value="158883629-700112812">158883629-700112812</option>
>> > > <option value="158924089-700099307">158924089-700099307</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/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/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: TypeError with 'dict'

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: [hidden email]
> To: [hidden email]
> CC: [hidden email]
> 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 <[hidden email]> 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, [hidden email]
> > <[hidden email]> 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
> > <[hidden email]>:
> >>
> >> 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: [hidden email]
> >> > To: [hidden email]; [hidden email]
> >> > 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"
> >> >
> >> > > <description>against hg19</description>
> >> > >
> >> > > <command interpreter="bash">screen_reads.sh $Project.input
> >> > > $Project.samples $Project $Samples </command>
> >> > >
> >> > > <inputs>
> >> > > <conditional name="Project">
> >> > > <param name="input" type="select" label="Select project">
> >> > > <option value="galaxy_test1">galaxy_test1</option>
> >> > > <option value="Untitled Folder">Untitled 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="147406386-700171390">147406386-700171390</option>
> >> > > <option value="158256496-700097688">158256496-700097688</option>
> >> > > <option value="158337416-700013715">158337416-700013715</option>
> >> > > <option value="158337416-700097837">158337416-700097837</option>
> >> > > <option value="158357646-700035237">158357646-700035237</option>
> >> > > <option value="158458797-700014562">158458797-700014562</option>
> >> > > <option value="158479027-700014724">158479027-700014724</option>
> >> > > <option value="158479027-700097196">158479027-700097196</option>
> >> > > <option value="158499257-700014837">158499257-700014837</option>
> >> > > <option value="158499257-700098561">158499257-700098561</option>
> >> > > <option value="158742018-700015181">158742018-700015181</option>
> >> > > <option value="158802708-700015245">158802708-700015245</option>
> >> > > <option value="158802708-700015250">158802708-700015250</option>
> >> > > <option value="158802708-700099803">158802708-700099803</option>
> >> > > <option value="158802708-700119165">158802708-700119165</option>
> >> > > <option value="158822939-700014954">158822939-700014954</option>
> >> > > <option value="158883629-700015113">158883629-700015113</option>
> >> > > <option value="158883629-700100227">158883629-700100227</option>
> >> > > <option value="158883629-700112812">158883629-700112812</option>
> >> > > <option value="158924089-700099307">158924089-700099307</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/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/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/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: TypeError with 'dict'

Martin Christiansen
Hi again,

Has anyone had time to look into the traceback?

Best,
Martin


From: [hidden email]
To: [hidden email]; [hidden email]
Date: Tue, 12 Aug 2014 15:59:53 +0200
CC: [hidden email]
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: [hidden email]
> To: [hidden email]
> CC: [hidden email]
> 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 <[hidden email]> 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, [hidden email]
> > <[hidden email]> 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
> > <[hidden email]>:
> >>
> >> 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: [hidden email]
> >> > To: [hidden email]; [hidden email]
> >> > 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"
> >> >
> >> > > <description>against hg19</description>
> >> > >
> >> > > <command interpreter="bash">screen_reads.sh $Project.input
> >> > > $Project.samples $Project $Samples </command>
> >> > >
> >> > > <inputs>
> >> > > <conditional name="Project">
> >> > > <param name="input" type="select" label="Select project">
> >> > > <option value="galaxy_test1">galaxy_test1</option>
> >> > > <option value="Untitled Folder">Untitled 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="147406386-700171390">147406386-700171390</option>
> >> > > <option value="158256496-700097688">158256496-700097688</option>
> >> > > <option value="158337416-700013715">158337416-700013715</option>
> >> > > <option value="158337416-700097837">158337416-700097837</option>
> >> > > <option value="158357646-700035237">158357646-700035237</option>
> >> > > <option value="158458797-700014562">158458797-700014562</option>
> >> > > <option value="158479027-700014724">158479027-700014724</option>
> >> > > <option value="158479027-700097196">158479027-700097196</option>
> >> > > <option value="158499257-700014837">158499257-700014837</option>
> >> > > <option value="158499257-700098561">158499257-700098561</option>
> >> > > <option value="158742018-700015181">158742018-700015181</option>
> >> > > <option value="158802708-700015245">158802708-700015245</option>
> >> > > <option value="158802708-700015250">158802708-700015250</option>
> >> > > <option value="158802708-700099803">158802708-700099803</option>
> >> > > <option value="158802708-700119165">158802708-700119165</option>
> >> > > <option value="158822939-700014954">158822939-700014954</option>
> >> > > <option value="158883629-700015113">158883629-700015113</option>
> >> > > <option value="158883629-700100227">158883629-700100227</option>
> >> > > <option value="158883629-700112812">158883629-700112812</option>
> >> > > <option value="158924089-700099307">158924089-700099307</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/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/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/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/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: TypeError with 'dict'

John Chilton-4
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
<[hidden email]> wrote:

> Hi again,
>
> Has anyone had time to look into the traceback?
>
> Best,
> Martin
>
> ________________________________
> From: [hidden email]
> To: [hidden email]; [hidden email]
> Date: Tue, 12 Aug 2014 15:59:53 +0200
>
> CC: [hidden email]
> 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: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>> 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 <[hidden email]> 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, [hidden email]
>> > <[hidden email]> 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
>> > <[hidden email]>:
>> >>
>> >> 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: [hidden email]
>> >> > To: [hidden email]; [hidden email]
>> >> > 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"
>> >> >
>> >> > > <description>against hg19</description>
>> >> > >
>> >> > > <command interpreter="bash">screen_reads.sh $Project.input
>> >> > > $Project.samples $Project $Samples </command>
>> >> > >
>> >> > > <inputs>
>> >> > > <conditional name="Project">
>> >> > > <param name="input" type="select" label="Select project">
>> >> > > <option value="galaxy_test1">galaxy_test1</option>
>> >> > > <option value="Untitled Folder">Untitled 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="147406386-700171390">147406386-700171390</option>
>> >> > > <option value="158256496-700097688">158256496-700097688</option>
>> >> > > <option value="158337416-700013715">158337416-700013715</option>
>> >> > > <option value="158337416-700097837">158337416-700097837</option>
>> >> > > <option value="158357646-700035237">158357646-700035237</option>
>> >> > > <option value="158458797-700014562">158458797-700014562</option>
>> >> > > <option value="158479027-700014724">158479027-700014724</option>
>> >> > > <option value="158479027-700097196">158479027-700097196</option>
>> >> > > <option value="158499257-700014837">158499257-700014837</option>
>> >> > > <option value="158499257-700098561">158499257-700098561</option>
>> >> > > <option value="158742018-700015181">158742018-700015181</option>
>> >> > > <option value="158802708-700015245">158802708-700015245</option>
>> >> > > <option value="158802708-700015250">158802708-700015250</option>
>> >> > > <option value="158802708-700099803">158802708-700099803</option>
>> >> > > <option value="158802708-700119165">158802708-700119165</option>
>> >> > > <option value="158822939-700014954">158822939-700014954</option>
>> >> > > <option value="158883629-700015113">158883629-700015113</option>
>> >> > > <option value="158883629-700100227">158883629-700100227</option>
>> >> > > <option value="158883629-700112812">158883629-700112812</option>
>> >> > > <option value="158924089-700099307">158924089-700099307</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/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/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/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/mailinglists/