Problem with RESCRIPT installation

Library Plugin Support
1

Hi I have some issues when installing RESCRIPt:
I used the following code from the RESCRIPt tutorial.

(qiime2-2023.2) zm@mendel:~/Sruta$ pip3 install git+https://github.com/bokulich-lab/RESCRIPt.git
Collecting git+https://github.com/bokulich-lab/RESCRIPt.git
  Cloning https://github.com/bokulich-lab/RESCRIPt.git to /home/zm/miniconda3/envs/qiime2-2023.2/syf/pip-req-build-zlf_6bmm
  Running command git clone --filter=blob:none --quiet https://github.com/bokulich-lab/RESCRIPt.git /home/zm/miniconda3/envs/qiime2-2023.2/syf/pip-req-build-zlf_6bmm
  Resolved https://github.com/bokulich-lab/RESCRIPt.git to commit fcfb9fecf7386cd0f8157c159bce1f3b836c2962
  Preparing metadata (setup.py) ... done
(qiime2-2023.2) zm@mendel:~/Sruta$ qiime rescript
Error: QIIME 2 has no plugin/command named 'rescript'.
(qiime2-2023.2) zm@mendel:~/Sruta$ qiime rescript get-silva-data \
>     --p-version '138.1' \
>     --p-target 'SSURef_NR99' \
>     --p-include-species-labels \
>     --o-silva-sequences silva-138.1-ssu-nr99-rna-seqs.qza \
>     --o-silva-taxonomy silva-138.1-ssu-nr99-tax.qza
Error: QIIME 2 has no plugin/command named 'rescript'.

Any help on this would be great.

Thanks

2

HI @Paulina_Srednicka ,
Thanks for trying out RESCRIPt :grin:

You are missing the last step after installing any plugin:

qiime dev refresh-cache

Give that a try and please let me know if you still get an error!

3

Hi @Nicholas_Bokulich,

after entering the command dev refresh-cache I recived an error. I cannot execute any commands in QIIME2 anymore, because this error show up... :frowning:

(qiime2-2022.8) zm@mendel:~$ qiime dev refresh-cache
QIIME 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/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/util.py", line 224, in get_plugin_manager
    return qiime2.sdk.PluginManager.reuse_existing()
  File "/home/zm/miniconda3/envs/qiime2-2022.8/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/zm/miniconda3/envs/qiime2-2022.8/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/builtin/dev.py", line 33, in refresh_cache
    import q2cli.core.cache
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/core/cache.py", line 285, in <module>
    CACHE = DeploymentCache()
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/core/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/core/cache.py", line 205, in _cache_current_state
    state = self._get_current_state()
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/core/cache.py", line 253, in _get_current_state
    plugin_manager = q2cli.util.get_plugin_manager()
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/util.py", line 236, in get_plugin_manager
    return qiime2.sdk.PluginManager()
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 67, in __new__
    self._init(add_plugins=add_plugins)
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
    plugin = entry_point.load()
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2471, in load
    return self.resolve()
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2477, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/rescript/plugin_setup.py", line 18, in <module>
    from .merge import merge_taxa
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/rescript/merge.py", line 14, in <module>
    from .ncbi import _allowed_ranks
  File "/home/zm/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/rescript/ncbi.py", line 18, in <module>
    from xmltodict import parse
ModuleNotFoundError: No module named 'xmltodict'
4

did you follow the full installation instructions? the error says that xmltodict is not installed, but this is the second step in the instructions.