Re: [galaxy-dev] Tool wrapper NotFound error

[John Chilton]

It looks like your library conditional is wrapped in a section called
"basicOptions". For this reason when it appears in your 
block you need to use $basicOptions.library.type for instance instead
of $library.type. Hope this helps and thanks for using Galaxy!

-John

On Wed, Oct 26, 2016 at 11:39 AM, evan clark  wrote:
> I have written  the below tool wrapper and when running in galaxy I receive
> the error. I am not sure the issue with the wrapper.
> 
>
> Traceback (most recent call last):
>   File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py",
> line 170, in prepare_job
> job_wrapper.prepare()
>   File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", line
> 897, in prepare
> self.command_line, self.extra_filenames, self.environment_variables =
> tool_evaluator.build()
>   File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/tools/evaluation.py",
> line 445, in build
> raise e
> NotFound: cannot find 'library'
>
> 
>
> 
> 
>
> Alternative splicing analysis
>
> python
> /home/eclark28/galaxy_production/python/lib/python2.7/site-packages/misopy/miso.py
> --version
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> Single-end
> Paired-end
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> ___
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[galaxy-dev] Tool wrapper NotFound error

[evan clark]

I have written  the below tool wrapper and when running in galaxy I 
receive the error. I am not sure the issue with the wrapper.



Traceback (most recent call last):
  File 
"/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py", 
line 170, in prepare_job

job_wrapper.prepare()
  File 
"/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", 
line 897, in prepare
self.command_line, self.extra_filenames, self.environment_variables 
= tool_evaluator.build()
  File 
"/home/eclark28/galaxy_production/galaxy/lib/galaxy/tools/evaluation.py", line 
445, in build

raise e
NotFound: cannot find 'library'






Alternative splicing analysis

python 
/home/eclark28/galaxy_production/python/lib/python2.7/site-packages/misopy/miso.py 
--version




















Single-end
Paired-end
























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[galaxy-dev] Error on chemfp version 1.1p1 installation

[Léo Biscassi]

Hi all,
I'm trying install chemical toolbox on a local instance and I got an error
the following error raised by chemfp dependency:


File 
"/home/leobiscassi/programs/galaxy-local/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
line 685, in execute_step
dir = self.url_download( work_dir, downloaded_filename, url,
extract=True, checksums=checksums )
  File 
"/home/leobiscassi/programs/galaxy-local/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
line 181, in url_download
raise Exception( err_msg )

Error downloading from URL
http://chem-fingerprints.googlecode.com/files/chemfp-1.1p1.tar.gz:
HTTP Error 404: Not Found

This link is the same it's in cargo-port [1], but isn't working, can you
help me?

[1] https://github.com/galaxyproject/cargo-port/blob/master/urls.tsv#L396
-- 
Best regards,
*Léo Biscassi*
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