Conda tutorial fixes. Enable --conda_use_local option for planemo test#876
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jmchilton merged 8 commits intogalaxyproject:masterfrom Nov 15, 2018
Merged
Conda tutorial fixes. Enable --conda_use_local option for planemo test#876jmchilton merged 8 commits intogalaxyproject:masterfrom
--conda_use_local option for planemo test#876jmchilton merged 8 commits intogalaxyproject:masterfrom
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The remaining test failures seem unrelated. |
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Yes, I think I fixed them in #874. |
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Rebased and green too! |
jmchilton
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Oct 30, 2018
| <tool id="fleeqtk_seq" name="Convert to FASTA (fleeqtk)" version="0.1.0"> | ||
| <requirements> | ||
| <requirement type="package" version="1.3">fleeqtk</requirement> | ||
| </requirements> |
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But this is part of the exercise right? Maybe make that more clear in the exercise written description?
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It is not mentioned anywhere in https://planemo.readthedocs.io/en/latest/writing_advanced.html#exercise-build-a-recipe , it's more of a surprise egg...
How to add a requirement was already explained for seqtk_seq using planemo tool_init in https://planemo.readthedocs.io/en/latest/writing_standalone.html#the-basics, it is not clear at all why it's removed here for fleeqtk_seq, unless the goal is to confuse people.
Without it, points 4 and 5 of https://planemo.readthedocs.io/en/latest/writing_advanced.html#exercise-build-a-recipe https://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html?highlight=fleeqtk#exercise-build-a-recipe would do nothing and fail respectively.
Skip `planemo conda_install` in conda tutorial which is not needed any more now.
It seems this never did what it was supposed to test.
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Follow up on commit 6047d8b .
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galaxyproject/galaxy#7013 should help for the failing tests. |
Fix the following traceback:
```
======================================================================
FAIL: Test training_generate_from_wf command with workflow on running instance.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/tests/test_cmd_training_generate_from_wf.py", line 77, in test_training_generate_from_wf_command_remote_wf
self._check_exit_code(training_init_command, exit_code=1)
File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/tests/test_utils.py", line 105, in _check_exit_code
return check_exit_code(self._runner, command_list, exit_code=exit_code)
File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/tests/test_utils.py", line 310, in check_exit_code
raise AssertionError(message)
AssertionError: Planemo command [training_generate_from_wf --topic_name test --tutorial_name test --workflow_id ID] resulted in unexpected exit code [-1], expected exit code [1]]. Command output [] Exception [The topic test does not exists. It should be created], Traceback [['Traceback (most recent call last):\n', ' File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/testing.py", line 279, in invoke\n prog_name=self.get_default_prog_name(cli), **extra)\n', ' File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/core.py", line 697, in main\n rv = self.invoke(ctx)\n', ' File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/core.py", line 1066, in invoke\n return _process_result(sub_ctx.command.invoke(sub_ctx))\n', ' File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/core.py", line 895, in invoke\n return ctx.invoke(self.callback, **ctx.params)\n', ' File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/core.py", line 535, in invoke\n return callback(*args, **kwargs)\n', ' File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/decorators.py", line 64, in new_func\n return ctx.invoke(f, obj, *args[1:], **kwargs)\n', ' File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/.venv3/lib/python3.5/site-packages/click/core.py", line 535, in invoke\n return callback(*args, **kwargs)\n', ' File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/planemo/cli.py", line 195, in handle_blended_options\n return f(*args, **kwds)\n', ' File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/planemo/commands/cmd_training_generate_from_wf.py", line 19, in cli\n training.generate_tuto_from_wf(ctx)\n', ' File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/planemo/training/__init__.py", line 86, in generate_tuto_from_wf\n self.check_topic_init_tuto()\n', ' File "/usr/users/ga002/soranzon/software/nsoranzo_planemo/planemo/training/__init__.py", line 45, in check_topic_init_tuto\n raise Exception("The topic %s does not exists. It should be created" % self.topic.name)\n', 'Exception: The topic test does not exists. It should be created\n']]
```
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