Question: planemo test --install_galaxy error
0
gravatar for domi84
9 months ago by
domi8440
Glasgow University
domi8440 wrote:

Hi,

I am trying to wrapping a tool for Galaxy.

I made a simple xml file with planemo and planemo lint is working fine as well.

(.venv) domenico@domenico-ThinkCentre-M93p:~$ planemo l
Linting tool /home/domenico/papillon.xml
Applying linter tests... CHECK
.. CHECK: 1 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 4 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.1.0].
.. CHECK: Tool defines a name [Read and plot cuffdiff data].
.. CHECK: Tool defines an id [papillon].
.. CHECK: Tool targets 16.01 Galaxy profile.
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... CHECK
.. CHECK: Found 1 likely valid citations.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.

But I am getting error with planemo test. So I tried only:

planemo test --install_galaxy

and I am getting the same error:

2018-01-16 15:41:17,924 INFO  [galaxy.model.migrate.check] Migrating 132 -> 133... 
2018-01-16 15:41:18,346 INFO  [galaxy.model.migrate.check] 
2018-01-16 15:41:18,347 INFO  [galaxy.model.migrate.check] Add dependencies column to jobs table
2018-01-16 15:41:18,347 INFO  [galaxy.model.migrate.check] 
2018-01-16 15:41:18,347 INFO  [galaxy.model.migrate.check] 
2018-01-16 15:41:18,347 INFO  [galaxy.model.migrate.check] Migrating 133 -> 134... 
2018-01-16 15:41:18,435 INFO  [galaxy.model.migrate.check] 
2018-01-16 15:41:18,435 INFO  [galaxy.model.migrate.check] Migration script to set the 'deleted' column of the
2018-01-16 15:41:18,435 INFO  [galaxy.model.migrate.check] 'history_dataset_association' table to True if 'purged' is True.
2018-01-16 15:41:18,436 INFO  [galaxy.model.migrate.check] 
2018-01-16 15:41:18,436 INFO  [galaxy.model.migrate.check] 
2018-01-16 15:41:18,436 INFO  [galaxy.model.migrate.check] Migrating 134 -> 135... 
2018-01-16 15:41:19,580 INFO  [galaxy.model.migrate.check] 
2018-01-16 15:41:19,580 INFO  [galaxy.model.migrate.check] This migration script adds support for storing tags in the context of a dataset in a library
2018-01-16 15:41:19,580 INFO  [galaxy.model.migrate.check] 
2018-01-16 15:41:19,580 INFO  [galaxy.model.migrate.check] 
2018-01-16 15:41:19,592 INFO  [galaxy.config] Install database targetting Galaxy's database configuration.
2018-01-16 15:41:20,017 ERROR [galaxy.visualization.genomes] Error reading twobit.loc
Traceback (most recent call last):
  File "/tmp/tmp5xv3auy3/galaxy-dev/lib/galaxy/visualization/genomes.py", line 211, in reload_genomes
    for line in open(os.path.join(self.app.config.tool_data_path, "twobit.loc")):
IOError: [Errno 2] No such file or directory: '/tmp/tmp5xv3auy3/galaxy-dev/tool-data/twobit.loc'
2018-01-16 15:41:20,060 INFO  [galaxy.util.handlers] Setting <handlers> default to child with id 'main'
2018-01-16 15:41:20,107 INFO  [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp5xv3auy3/tool_conf.xml
2018-01-16 15:41:20,119 INFO  [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp5xv3auy3/shed_tools_conf.xml
2018-01-16 15:41:20,119 INFO  [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp5xv3auy3/empty_tool_conf.xml
No handlers could be found for logger "galaxy.datatypes.display_applications.application"
2018-01-16 15:41:20,330 INFO  [galaxy.jobs] Handler 'main' will load all configured runner plugins
2018-01-16 15:41:20,334 INFO  [galaxy.jobs.handler] job handler stop queue started
2018-01-16 15:41:20,344 INFO  [galaxy.jobs.handler] job handler queue started
2018-01-16 15:41:20,356 INFO  [galaxy.app] Galaxy app startup finished (130082.764 ms)
2018-01-16 15:41:20,846 INFO  [galaxy.queue_worker] Binding and starting galaxy control worker for main
/home/domenico/.planemo/gx_venv/local/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate.  Consider alternative strategies for improved performance.
  'strategies for improved performance.' % expr)

----------------------------------------------------------------------
XML: /tmp/tmp5xv3auy3/xunit.xml
----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK
2018-01-16 15:41:21,619 INFO  [test_driver] Shutting down
2018-01-16 15:41:21,619 INFO  [test_driver] Shutting down embedded galaxy web server
2018-01-16 15:41:21,620 INFO  [test_driver] Embedded web server galaxy stopped
2018-01-16 15:41:21,620 INFO  [test_driver] Stopping application galaxy
2018-01-16 15:41:24,062 INFO  [galaxy.jobs.handler] sending stop signal to worker thread
2018-01-16 15:41:24,062 INFO  [galaxy.jobs.handler] job handler queue stopped
2018-01-16 15:41:24,062 INFO  [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads
2018-01-16 15:41:24,063 INFO  [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads
2018-01-16 15:41:24,063 INFO  [galaxy.jobs.handler] sending stop signal to worker thread
2018-01-16 15:41:24,063 INFO  [galaxy.jobs.handler] job handler stop queue stopped
2018-01-16 15:41:24,063 INFO  [test_driver] Application galaxy stopped.
2018-01-16 15:41:24,064 INFO  [galaxy.jobs.handler] sending stop signal to worker thread
2018-01-16 15:41:24,064 INFO  [galaxy.jobs.handler] job handler queue stopped
2018-01-16 15:41:24,064 INFO  [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads
2018-01-16 15:41:24,065 INFO  [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads
2018-01-16 15:41:24,065 INFO  [galaxy.jobs.handler] sending stop signal to worker thread
2018-01-16 15:41:24,065 INFO  [galaxy.jobs.handler] job handler stop queue stopped
Testing complete. HTML report is in "/home/domenico/tool_test_output.html".

It seems an Error reading twobit.loc , isn't? I opened the tool_test_output.html file, but it is empty:

Overview

No tests were executed.

Tests

The remainder of this contains a description for each test executed to run these jobs.

What should I do? Thanks

planemo • 283 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by domi8440
1
gravatar for domi84
9 months ago by
domi8440
Glasgow University
domi8440 wrote:

I fixed it deleting .venv and .planemo folders, and doing it again: so:

virtualenv .venv; . .venv/bin/activate
pip install planemo
planemo t --install_galaxy

and it worked

ADD COMMENTlink written 9 months ago by domi8440

Thanks for posting the solution back and glad that worked out!

ADD REPLYlink written 9 months ago by Jennifer Hillman Jackson25k
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