Question: Problems with trim galore in galaxy
1
gravatar for beth.rusnak
21 months ago by
beth.rusnak10
beth.rusnak10 wrote:

I've tried to install trim galore in galaxy (several different versions). All my other tools install fine but this one crashed with

xxxx - - [07/Apr/2016:10:50:54 -0400] "POST /tool_runner/index HTTP/1.1" 200 - "http://xxxxu:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftrim_galore%2Ftrim_galore%2F0.4.2" "Mozilla/5.0 (X11; Linux x86_64; rv:38.0) Gecko/20100101 Firefox/38.0"
10.16.40.19 - - [07/Apr/2016:10:50:54 -0400] "GET /api/histories/2faba7054d92b2df/contents HTTP/1.1" 200 - "http://hybrid.dhe.duke.edu:8080/" "Mozilla/5.0 (X11; Linux x86_64; rv:38.0) Gecko/20100101 Firefox/38.0"
galaxy.jobs.runners ERROR 2016-04-07 10:50:54,822 (177) Failure preparing job
Traceback (most recent call last):
  File "/analysis/GALAXY/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 157, in prepare_job
    job_wrapper.prepare()
  File "/analysis/GALAXY/galaxy-dist/lib/galaxy/jobs/__init__.py", line 828, in prepare
    self.command_line, self.extra_filenames = tool_evaluator.build()
  File "/analysis/is/GALAXY/galaxy-dist/lib/galaxy/tools/evaluation.py", line 371, in build
    self.__build_command_line( )
  File "/analysis/GALAXY/galaxy-dist/lib/galaxy/tools/evaluation.py", line 387, in __build_command_line
    command_line = fill_template( command, context=param_dict )
  File "/analysis/GALAXY/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/analysis/GALAXY/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1460040292_92_74170.py", line 145, in respond
NotFound: cannot find '__tool_directory__'

cutadapt has installed correctly and I just can't figure this out!

galaxy • 487 views
ADD COMMENTlink modified 21 months ago by Martin Čech ♦♦ 4.3k • written 21 months ago by beth.rusnak10
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