installation issue

[yuvaramsingh94]

Hi,
i am trying to install CAP2 by following the steps provided here. the installation is throwing the following error which i am not able to fix. i tried on python 3.8, 3.9.
`
File "/data/yuvaram/conda_installation/miniconda3/envs/test_2/lib/python3.8/site-packages/cap2-0.4.1-
py3.8.egg/cap2/capalyzer/pangea/parsers.py", line 3
import ..parsers as local_parsers
^
SyntaxError: invalid syntax

`

[dcdanko]

What version of the CAP?

[yuvaramsingh94]

i am trying to install CAP2. due to this issue, i am not able to get a full installation.

[yuvaramsingh94]

@dcdanko also tried with Docker image provided here. but, this image also failed while running python -m pytest tests
is there any updated docker image or repo for installing CAP2 as we are trying to run CAP2 pipeline on our data.

`
===== Luigi Execution Summary =====
============================================================================================= warnings summary =============================================================================================
../../root/miniconda3/lib/python3.8/site-packages/luigi/freezing.py:7
/root/miniconda3/lib/python3.8/site-packages/luigi/freezing.py:7: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will stop working
from collections import OrderedDict, Mapping

../../root/miniconda3/lib/python3.8/site-packages/luigi/init.py:78
/root/miniconda3/lib/python3.8/site-packages/luigi/init.py:78: DeprecationWarning:
Autoloading range tasks by default has been deprecated and will be removed in a future version.
To get the behavior now add an option to luigi.cfg:

          [core]
            autoload_range: false

        Alternately set the option to true to continue with existing behaviour and suppress this warning.
    
  warnings.warn(warning_message, DeprecationWarning)

../../root/miniconda3/lib/python3.8/site-packages/Bio/Alphabet/init.py:22
/root/miniconda3/lib/python3.8/site-packages/Bio/Alphabet/init.py:22: PendingDeprecationWarning: We intend to remove or replace Bio.Alphabet in 2020, ideally avoid using it explicitly in your code. Please get in touch if you will be adversely affected by this. biopython/biopython#2046
warnings.warn("We intend to remove or replace Bio.Alphabet in 2020, "

tests/test_api.py::TestApi::test_qc_stage
tests/test_experimental_covid.py::TestCovidPipeline::test_pre_task_list_pangea
/root/miniconda3/lib/python3.8/site-packages/luigi/parameter.py:279: UserWarning: Parameter "python" with value "3" is not of type string.
warnings.warn('Parameter "{}" with value "{}" is not of type string.'.format(param_name, param_value))

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================================================================================= short test summary info ==========================================================================================
FAILED tests/test_experimental_covid.py::TestCovidPipeline::test_align_to_covid_genome - AssertionError: False is not true
FAILED tests/test_experimental_covid.py::TestCovidPipeline::test_covid_consensus_seq - AssertionError: False is not true
FAILED tests/test_experimental_covid.py::TestCovidPipeline::test_covid_variants - AssertionError: False is not true
FAILED tests/test_experimental_covid.py::TestCovidPipeline::test_make_pileup - AssertionError: False is not true
FAILED tests/test_experimental_strain.py::TestStrainPipeline::test_align_to_genome - AssertionError: False is not true
FAILED tests/test_experimental_strain.py::TestStrainPipeline::test_make_pileup - AssertionError: False is not true
FAILED tests/test_pipeline_preprocessing.py::TestPipelinePreprocessing::test_adapter_remove_reads - AssertionError: False is not true
FAILED tests/test_pipeline_preprocessing.py::TestPipelinePreprocessing::test_fast_taxa - AssertionError: False is not true
FAILED tests/test_pipeline_preprocessing.py::TestPipelinePreprocessing::test_invoke_remove_human_reads - AssertionError: False is not true
FAILED tests/test_pipeline_preprocessing.py::TestPipelinePreprocessing::test_invoke_remove_mouse_reads - AssertionError: False is not true
==================================================================== 10 failed, 42 passed, 11 skipped, 5 warnings in 307.04s (0:05:07) =====================================================================

`

[yuvaramsingh94]

@dcdanko i am using version='0.4.1'.