Hello again,
I tried to run the command you provided. But I didn't have a good time installing RESCRIPt. I need to install it in qiime2. I'm using version 2021.2 and running on the Oracle VM VirtualBox.
Next, I follow the tutorial in the website to install (GitHub - bokulich-lab/RESCRIPt: REference Sequence annotation and CuRatIon Pipeline).
conda activate qiime2-2021.2
conda install -c conda-forge -c bioconda -c qiime2 -c defaults xmltodict
I ran these two commands and the following appeared:
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.9.2
latest version: 4.10.1
Please update conda by running
$ conda update -n base -c defaults conda
Package Plan
environment location: /home/qiime2/miniconda/envs/qiime2-2021.2
added / updated specs:
- xmltodict
The following packages will be downloaded:
package | build
---------------------------|-----------------
openssl-1.1.1k | h7f98852_0 2.1 MB conda-forge
xmltodict-0.12.0 | py_0 11 KB conda-forge
------------------------------------------------------------
Total: 2.1 MB
The following NEW packages will be INSTALLED:
xmltodict conda-forge/noarch::xmltodict-0.12.0-py_0
The following packages will be UPDATED:
certifi pkgs/main::certifi-2020.12.5-py36h06a~ --> conda-forge::certifi-2020.12.5-py36h5fab9bb_1
openssl pkgs/main::openssl-1.1.1j-h27cfd23_0 --> conda-forge::openssl-1.1.1k-h7f98852_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2021.1.19-~ --> conda-forge::ca-certificates-2020.12.5-ha878542_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
xmltodict-0.12.0 | 11 KB | ###################################################################################################################### | 100%
openssl-1.1.1k | 2.1 MB | ###################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
And then, I ran the command:
conda update -n base -c defaults conda
pip install git+https://github.com/bokulich-lab/RESCRIPt.git
After running the two commands, the following is displayed:
Collecting git+https://github.com/bokulich-lab/RESCRIPt.git
Cloning GitHub - bokulich-lab/RESCRIPt: REference Sequence annotation and CuRatIon Pipeline to /tmp/pip-req-build-kxpa30gs
Running command git clone -q GitHub - bokulich-lab/RESCRIPt: REference Sequence annotation and CuRatIon Pipeline /tmp/pip-req-build-kxpa30gs
Building wheels for collected packages: rescript
Building wheel for rescript (setup.py) ... done
Created wheel for rescript: filename=rescript-2021.4.0.dev0+6.g073ccf0-py3-none-any.whl size=157116 sha256=1d9116e47ba5170f2a2a849c4b347107279627a7f457900586111a804aaa68ee
Stored in directory: /tmp/pip-ephem-wheel-cache-2r0x4srb/wheels/db/0b/eb/f9d025609a8a1939d5ada85024251d0a18aff46b24d8170b47
Successfully built rescript
Installing collected packages: rescript
Successfully installed rescript-2021.4.0.dev0+6.g073ccf0
I thought I had rescript installed correctly, so I started processing my data. But no matter what command I type next, it will show an error. The tips are as follows:
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/qiime2/miniconda/envs/qiime2-2021.2/bin/qiime", line 11, in
sys.exit(qiime())
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/click/core.py", line 1254, in invoke
cmd_name, cmd, args = self.resolve_command(ctx, args)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/click/core.py", line 1297, in resolve_command
cmd = self.get_command(ctx, cmd_name)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/commands.py", line 100, in get_command
plugin = self._plugin_lookup[name]
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
import q2cli.core.cache
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/core/cache.py", line 406, in
CACHE = DeploymentCache()
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/core/cache.py", line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/core/cache.py", line 200, in _cache_current_state
state = self._get_current_state()
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/core/cache.py", line 238, in _get_current_state
plugin_manager = qiime2.sdk.PluginManager()
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 54, in new
self._init(add_plugins=add_plugins)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 81, in _init
plugin = entry_point.load()
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pkg_resources/init.py", line 2472, in load
return self.resolve()
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pkg_resources/init.py", line 2478, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/rescript/plugin_setup.py", line 24, in
from .get_data import get_silva_data
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/rescript/get_data.py", line 19, in
from q2_types.feature_data import RNAFASTAFormat
ImportError: cannot import name 'RNAFASTAFormat'
Why? Is it because the tutorial is only available for version 2021.4 of qiime2? But I see that the official website has not been updated to 2021.4(https://s3-us-west-2.amazonaws.com/qiime2-data/distro/core/virtualbox-images.txt).
Looking forward to your reply, thank you!