Hi Marius,
It'd be great if you wanted to submit a PR for the json issue separately --
I can confirm that that's a working fix. I'll let someone else speak to
the tool change.
-Dannon
On Thu, Apr 30, 2015 at 2:30 PM Marius van den Beek <m.vandenb...@gmail.com>
wrote:
> Hello all,
>
> Not sure if the mailing list or trello would be appropriate for this.
> I had a problem using the gff_filter_by_attribute tool, both locally and
> on usegalaxy.org.
> Neither filtering for GTF or GFF were working.
>
> The error message was:
>
> Traceback (most recent call last):
> File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line
> 158, in prepare_job
> job_wrapper.prepare()
> File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 832, in
> prepare
> self.command_line, self.extra_filenames = tool_evaluator.build()
> File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 408,
> in build
> self.__build_command_line( )
> File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 424,
> in __build_command_line
> command_line = fill_template( command, context=param_dict )
> File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in
> fill_template
> return str( Template( source=template_text, searchList=[context] ) )
> File
> "/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py",
> line 1004, in __str__
> return getattr(self, mainMethName)()
> File "DynamicallyCompiledCheetahTemplate.py", line 92, in respond
> NotFound: cannot find 'attribute_types' while searching for
> 'input.metadata.attribute_types'
>
>
> I could fix it by importing safe_dumps from galaxy.util.json, which
> apparently was not imported.
> The next problem occurred because gff_filter_by_attribute expects GTF
> attribute name-value separators (" ") but allowed GFF input, which uses
> ("=") as separator. I added a logic to switch
> between seperators based on the file extension. Everything works smoothly
> now,
> the code changes are here:
> https://github.com/mvdbeek/galaxy
> Should I create a pull request?
>
> --
> Marius van den Beek, PhD
>
> Drosophila Genetics and Epigenetics
> Institut de Biologie Paris Seine
> <http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile>
> 9, Quai St Bernard, Boîte courrier 24
> 75252 Paris Cedex 05
> Tel +33 01 44 27 34 01
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
