Hi,
I know my question has been posted many times, and I really tried the suggested solutions but so far nothing works.
I tried to install using biconda, but failed.
Then I installed picrust2 from source using this:
wget https://github.com/picrust/picrust2/archive/v2.4.2.tar.gz
tar xvzf v2.4.2.tar.gz
cd picrust2-2.4.2/
conda env create -f picrust2-env.yaml
conda activate picrust2
pip install --editable
then got this:
Usage:
pip install [options] [package-index-options] ...
pip install [options] -r [package-index-options] ...
pip install [options] [-e] ...
pip install [options] [-e] ...
pip install [options] <archive url/path> ...
--editable option requires 1 argument
Then when I ran pytest, I got this long failure message:
FileNotFoundError: [Errno 2] No such file or directory: 'picrust2_pipeline.py'
../miniconda3/envs/picrust2/lib/python3.8/subprocess.py:1704: FileNotFoundError
=============================== warnings summary ===============================
tests/test_pathway_pipeline.py: 54 warnings
/home/raizada/picrust2-2.4.2/picrust2/pathway_pipeline.py:1243: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
new_df = new_df.append(new_subset)
-- Docs: How to capture warnings — pytest documentation
=========================== short test summary info ============================
FAILED tests/test_workflow.py::workflow_test::test_full_pipeline_tsv - FileNo...
FAILED tests/test_workflow.py::workflow_test::test_help_calls - FileNotFoundE...
FAILED tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script
FAILED tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script_per_seq_contrib_strat
FAILED tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script_per_seq_contrib_strat_skip_norm
================== 5 failed, 56 passed, 54 warnings in 39.42s ==================
So, I deactivated picrust env then removed it, and activated qiime2-2022.2 env and installed picrust (cd picrust2-2.4.2/) using this:
conda install q2-picrust2=2021.11_0 -c conda-forge -c bioconda -c gavinmdouglas
Then I got repeated failure message:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
So, I tested picrust in qiime2 env by pytest, and got this
FileNotFoundError: [Errno 2] No such file or directory: 'picrust2_pipeline.py'
../miniconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py:1704: FileNotFoundError
=========================== short test summary info ============================
FAILED tests/test_hsp.py::castor_hsp_workflow_tests::test_emp_prob_ci - Syste...
FAILED tests/test_hsp.py::castor_hsp_workflow_tests::test_emp_prob_simple - S...
FAILED tests/test_hsp.py::castor_hsp_workflow_tests::test_mp_simple - SystemE...
FAILED tests/test_hsp.py::castor_hsp_workflow_tests::test_nsti - SystemExit: 1
FAILED tests/test_hsp.py::castor_hsp_workflow_tests::test_pic_simple - System...
FAILED tests/test_hsp.py::castor_hsp_workflow_tests::test_scp_simple - System...
FAILED tests/test_hsp.py::castor_hsp_workflow_tests::test_subtree_average_simple
FAILED tests/test_pathway_pipeline.py::run_minpath_tests::test_strat_default_pipeline_wide
FAILED tests/test_pathway_pipeline.py::run_minpath_tests::test_strat_per_genome_pipeline
FAILED tests/test_pathway_pipeline.py::run_minpath_tests::test_strat_per_genome_pipeline_strat_input
FAILED tests/test_pathway_pipeline.py::run_minpath_tests::test_unstrat_default_pipeline
FAILED tests/test_place_seqs.py::place_seqs_tests::test_gappa_jplace_to_newick
FAILED tests/test_place_seqs.py::place_seqs_tests::test_run_epa_ng - FileNotF...
FAILED tests/test_place_seqs.py::place_seqs_tests::test_run_place_seqs_pipeline_epa_ng
FAILED tests/test_place_seqs.py::place_seqs_tests::test_run_place_seqs_pipeline_sepp
FAILED tests/test_workflow.py::workflow_test::test_full_pipeline_tsv - FileNo...
FAILED tests/test_workflow.py::workflow_test::test_help_calls - FileNotFoundE...
FAILED tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script
FAILED tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script_per_seq_contrib_strat
FAILED tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script_per_seq_contrib_strat_skip_norm
======================== 20 failed, 41 passed in 33.55s =======================
So, it seems that installing picrust in a new picrust env is better than installing in qiime env??
Also, I am wondering if [PICRUSt2 v2.4.2] is compatible with Qiime2-2022.2 or not??
Any help, please!