problem qiime2 2023.5

iordanis · July 18, 2024, 2:05pm

Hello every one i have one problem

I wan try to install rescript plugin into my env qiime2 2023.5 from here: RESCRIPt/install-prior-versions.md at master · bokulich-lab/RESCRIPt · GitHub

and know any time i wright qiime --hlep i have this issue or when activate my conda env

IIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/util.py", line 266, in get_plugin_manager
return qiime2.sdk.PluginManager.reuse_existing()
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 58, in reuse_existing
raise UninitializedPluginManagerError
qiime2.sdk.plugin_manager.UninitializedPluginManagerError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/admin1/miniconda3/envs/qiime2-2023.5/bin/qiime", line 11, in
sys.exit(qiime())
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1054, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 920, in make_context
self.parse_args(ctx, args)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1613, in parse_args
rest = super().parse_args(ctx, args)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1378, in parse_args
value, args = param.handle_parse_result(ctx, opts, args)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 2360, in handle_parse_result
value = self.process_value(ctx, value)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 2322, in process_value
value = self.callback(ctx, self, value)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1273, in show_help
echo(ctx.get_help(), color=ctx.color)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 699, in get_help
return self.command.get_help(self)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1298, in get_help
self.format_help(ctx, formatter)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1331, in format_help
self.format_options(ctx, formatter)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/click/command.py", line 157, in format_options
for subcommand in self.list_commands(ctx):
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/commands.py", line 92, in list_commands
plugins = sorted(self._plugin_lookup)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
import q2cli.core.cache
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 285, in
CACHE = DeploymentCache()
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 205, in _cache_current_state
state = self._get_current_state()
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 253, in _get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/util.py", line 278, in get_plugin_manager
return qiime2.sdk.PluginManager()
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 67, in new
self._init(add_plugins=add_plugins)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
plugin = entry_point.load()
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/pkg_resources/init.py", line 2517, in load
return self.resolve()
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/pkg_resources/init.py", line 2523, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/admin1/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/rescript/plugin_setup.py", line 11, in
from q2_types.genome_data import GenomeData, Loci, Proteins
ModuleNotFoundError: No module named 'q2_types.genome_data'

Any help pliz!

SoilRotifer · July 18, 2024, 2:45pm

Hi @iordanis,

It'd be easiest to simply download and install the latest version of QIIME 2, as RESCRIPt is already included.

Anyway, what commands did you run?

Try running the following within your 2023.5 environment:

conda activate qiime2-2023.5

conda install -c conda-forge -c bioconda -c qiime2 \
    -c https://packages.qiime2.org/qiime2/2023.5/passed/ \
    -c defaults xmltodict 'q2-types-genomics>2023.2' ncbi-datasets-pylib

Give this a try and let us know if it works. If not try using tested in place of passed on the second line.

iordanis · July 18, 2024, 5:01pm

Hi @SoilRotifer

Yes this i run this command after that i run qiime2 --help and rescript ans the plugin was not in.
Then i run the command : ```
pip install git+https://github.com/bokulich-lab/RESCRIPt.git

from this point when i activate the conda env i receive again and again the aboves!

BEST
Jordan

SoilRotifer · July 18, 2024, 6:18pm

I think the pip install is the problem here, as it is pulling from the most current version of RESCRIPt, which is likely incompatible. I'd suggest downloading the 2023.5 release files from here, then run pip install from within the RESCRIPt-2023.5.0 folder.

iordanis · July 19, 2024, 9:35am

Hi @SoilRotifer ,

did you mean this comand?

Option 2: Install within QIIME 2 environment
First activate your QIIME 2 environment (ver 2022.8 or later) and install relevant dependencies:

conda activate qiime2-2023.2
conda install -c conda-forge -c bioconda -c qiime2 -c https://packages.qiime2.org/qiime2/2023.5/tested/ -c defaults \
  xmltodict 'q2-types-genomics>2023.2' ncbi-datasets-pylib

Install source:

pip install git+https://github.com/bokulich-lab/RESCRIPt.git

from the Source code(zip)

Best
Jordan

SoilRotifer · July 19, 2024, 3:00pm

I guess there is a typo in the README, it should say 2023.5.

It should be:

conda activate qiime2-2023.5

conda install -c conda-forge -c bioconda -c qiime2 -c https://packages.qiime2.org/qiime2/2023.5/tested/ -c defaults \
  xmltodict 'q2-types-genomics>2023.2' ncbi-datasets-pylib

Then go into the source directory RESCRIPt-2023.5.0, and run pip install . This will install that specific version of RESCRPt. Otherwise installing via the git+ https will install the latest version which is not compatible with your version.

Again, it'd be much easier if you simply installed the latest version of QIIME 2, as RESCRIPt is part of the install now. Remember you can have multiple installs of QIIME 2 as separate conda environments and switch between them as needed.

-Mike

iordanis · July 19, 2024, 3:05pm

Hi @SoilRotifer

Ok i will do this!!!

thank you for the help.

Best
Jordan

system · August 19, 2024, 9:05pm

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