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picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2
GNU General Public License v3.0
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Error in Picrust2_pipeline.py #325

Closed Mirabelle0116 closed 8 months ago

Mirabelle0116 commented 1 year ago

Hello!!!! when I use function picrust2_pipeline.py ,here is an error Traceback (most recent call last): File "/home/data/t060452/.local/bin/picrust2_pipeline.py", line 4, in import('pkg_resources').require('PICRUSt2==2.5.2') File "/usr/local/lib/python3.8/dist-packages/pkg_resources/init.py", line 3324, in def _initialize_master_working_set(): File "/usr/local/lib/python3.8/dist-packages/pkg_resources/init.py", line 3298, in _call_aside f(*args, **kwargs) File "/usr/local/lib/python3.8/dist-packages/pkg_resources/init.py", line 3336, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/usr/local/lib/python3.8/dist-packages/pkg_resources/init.py", line 629, in _build_master ws.require(requires) File "/usr/local/lib/python3.8/dist-packages/pkg_resources/init.py", line 966, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/local/lib/python3.8/dist-packages/pkg_resources/init.py", line 827, in resolve dist = self._resolve_dist( File "/usr/local/lib/python3.8/dist-packages/pkg_resources/init.py", line 868, in _resolve_dist raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'PICRUSt2==2.5.2' distribution was not found and is required by the application

when I use pytest,the errors are as follows: FAILED picrust2-2.5.2/tests/test_place_seqs.py::place_seqs_tests::test_run_place_seqs_pipeline_sepp - SystemExit: 1 FAILED picrust2-2.5.2/tests/test_workflow.py::workflow_test::test_full_pipeline_tsv - SystemExit: 1 FAILED picrust2-2.5.2/tests/test_workflow.py::workflow_test::test_help_calls - SystemExit: 1 FAILED picrust2-2.5.2/tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script - SystemExit: 1 FAILED picrust2-2.5.2/tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script_per_seq_contrib_strat - SystemExit: 1 FAILED picrust2-2.5.2/tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script_per_seq_contrib_strat_skip_norm - SystemExit: 1

So what should I do in order to use the function picrust2_pipeline.py?
Thanks. All the best.

R-Wright-1 commented 1 year ago

Hi, it looks like when you're running the picrust2_pipeline.py script, it isn't able to find the PICRUSt2 package. Did you follow the instructions here for installing PICRUSt2? Perhaps you installed the package in a conda/mamba environment and need to activate this prior to running the script, or maybe you moved the script and it isn't able to find the full package?

R-Wright-1 commented 8 months ago

I am just closing this issue as there hasn't been any follow-up for a while. Please let me know if this needs to be reopened.