issues with qiime2 install

Hi I tried installing based on this link:
https://docs.qiime2.org/2020.2/install/native/

It has an error at this step:
conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-osx-conda.yml

Thank you!

(base) MacBook-Pro:~ user$ conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-osx-conda.yml

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
        return func(*args, **kwargs)
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 80, in do_call
        exit_code = getattr(module, func_name)(args, parser)
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 80, in execute
        directory=os.getcwd())
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/specs/__init__.py", line 40, in detect
        if spec.can_handle():
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/specs/yaml_file.py", line 18, in can_handle
        self._environment = env.from_file(self.filename)
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/env.py", line 151, in from_file
        return from_yaml(yamlstr, filename=filename)
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/env.py", line 136, in from_yaml
        data = yaml_load_standard(yamlstr)
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda/common/serialize.py", line 76, in yaml_load_standard
        return yaml.load(string, Loader=yaml.Loader, version="1.2")
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/main.py", line 935, in load
        return loader._constructor.get_single_data()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/constructor.py", line 109, in get_single_data
        node = self.composer.get_single_node()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/composer.py", line 78, in get_single_node
        document = self.compose_document()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/composer.py", line 104, in compose_document
        self.parser.get_event()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/parser.py", line 163, in get_event
        self.current_event = self.state()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/parser.py", line 239, in parse_document_end
        token = self.scanner.peek_token()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/scanner.py", line 182, in peek_token
        self.fetch_more_tokens()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/scanner.py", line 282, in fetch_more_tokens
        return self.fetch_value()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/scanner.py", line 655, in fetch_value
        self.reader.get_mark(),
    ruamel_yaml.scanner.ScannerError: mapping values are not allowed here
      in "<unicode string>", line 4, column 56:
         ... cted automatically to target URL: <a href="https://raw.githubuse ... 
                                             ^ (line: 4)

`$ /Users/user/opt/miniconda3/bin/conda-env create -n qiime2-2020.2 --file qiime2-2020.2-py36-osx-conda.yml`

  environment variables:
                 CIO_TEST=<not set>
  CONDA_AUTO_UPDATE_CONDA=false
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/Users/user/opt/miniconda3/bin/conda
             CONDA_PREFIX=/Users/user/opt/miniconda3
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/Users/user/opt/miniconda3/bin/python
               CONDA_ROOT=/Users/user/opt/miniconda3
              CONDA_SHLVL=1
                     PATH=/Users/user/opt/miniconda3/bin:/Users/user/opt/miniconda3/
                          bin:/Users/user/opt/miniconda3/condabin:/Library/Frameworks/Pyth
                          on.framework/Versions/3.8/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/
                          sbin:/Library/TeX/texbin:/opt/X11/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : base
    active env location : /Users/user/opt/miniconda3
            shell level : 1
       user config file : /Users/user/.condarc
 populated config files : /Users/user/.condarc
          conda version : 4.8.2
    conda-build version : not installed
         python version : 3.7.6.final.0
       virtual packages : __osx=10.14.6
       base environment : /Users/user/opt/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/anaconda/osx-64
                          https://conda.anaconda.org/anaconda/noarch
                          https://conda.anaconda.org/biocore/osx-64
                          https://conda.anaconda.org/biocore/noarch
                          https://conda.anaconda.org/bioconda/osx-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/qiime2/osx-64
                          https://conda.anaconda.org/qiime2/noarch
                          https://conda.anaconda.org/qiime2/label/r2020.2/osx-64
                          https://conda.anaconda.org/qiime2/label/r2020.2/noarch
          package cache : /Users/user/opt/miniconda3/pkgs
                          /Users/user/.conda/pkgs
       envs directories : /Users/user/opt/miniconda3/envs
                          /Users/user/.conda/envs
               platform : osx-64
             user-agent : conda/4.8.2 requests/2.23.0 CPython/3.7.6 Darwin/18.7.0 OSX/10.14.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Hello Elizabeth,

Welcome to the Qiime 2 forums. :qiime2: Thanks for posting the detailed error message.

I’ve received errors like this when my qiime2-2020.2-py36-osx-conda.yml was messed up or didn’t fully download. Could you post the last few lines of that file just to make sure it looks alright?

tail qiime2-2020.2-py36-osx-conda.yml

Thanks,
Colin

This is what the yml file says (tail just prints this):

Redirecting...

Redirecting...

You should be redirected automatically to target URL: https://raw.githubusercontent.com/qiime2/environment-files/master/2020.2/release/qiime2-2020.2-py36-osx-conda.yml. If not click the link.

And points me to this file:
https://raw.githubusercontent.com/qiime2/environment-files/master/2020.2/release/qiime2-2020.2-py36-osx-conda.yml

I also tried just running these commands directly, and I get the same error.

Thanks!

Yeah, it looks like that file failed to download…

Do you have wget installed?

You can run the command by itself, just to make sure it’s working. I have it installed and it shows me this:

(base) %> wget
wget: missing URL
Usage: wget [OPTION]... [URL]...

Try `wget --help' for more options.

Colin