cannot install

[pavlo888]

Hi @oschwengers

I am very excited to use this tool for plasmid reconstruction. However, I am having some issue installing the package.

As of now, I have tried installing it via Conda with the following command:
conda env create --prefix ~/tmp/conda-envs/tadrep/ --file environment.yml

But then I get an error with a long message:
`# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1118, in __call__
    return func(*args, **kwargs)
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 78, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/conda/notices/core.py", line 109, in wrapper
    return func(*args, **kwargs)
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 101, in execute
    spec = specs.detect(name=name, filename=get_filename(args.file), directory=os.getcwd())
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/conda_env/specs/__init__.py", line 46, in detect
    if spec.can_handle():
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/conda_env/specs/yaml_file.py", line 18, in can_handle
    self._environment = env.from_file(self.filename)
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/conda_env/env.py", line 169, in from_file
    return from_yaml(yamlstr, filename=filename)
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/conda_env/env.py", line 143, in from_yaml
    data = yaml_safe_load(yamlstr)
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 67, in yaml_safe_load
    return _yaml_safe().load(string)
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/ruamel/yaml/main.py", line 434, in load
    return constructor.get_single_data()
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/ruamel/yaml/constructor.py", line 119, in get_single_data
    node = self.composer.get_single_node()
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/ruamel/yaml/composer.py", line 76, in get_single_node
    document = self.compose_document()
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/ruamel/yaml/composer.py", line 99, in compose_document
    node = self.compose_node(None, None)
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/ruamel/yaml/composer.py", line 143, in compose_node
    node = self.compose_mapping_node(anchor)
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/ruamel/yaml/composer.py", line 216, in compose_mapping_node
    while not self.parser.check_event(MappingEndEvent):
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/ruamel/yaml/parser.py", line 146, in check_event
    self.current_event = self.state()
  File "/Users/pavlo/opt/anaconda3/lib/python3.9/site-packages/ruamel/yaml/parser.py", line 753, in parse_flow_mapping_key
    raise ParserError(
ruamel.yaml.parser.ParserError: while parsing a flow mapping
  in "<unicode string>", line 1, column 1:
    {\rtf1\ansi\ansicpg1252\cocoartf2639
    ^ (line: 1)
expected ',' or '}', but got '{'
  in "<unicode string>", line 2, column 34:
    \cocoatextscaling0\cocoaplatform0{\fonttbl\f0\fmodern\fcharset0 C ... 
                                     ^ (line: 2)

$ /Users/pavlo/opt/anaconda3/bin/conda-env create --prefix /Users/pavlo/tmp/conda-envs/tadrep/ --file environment.yml

environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=base
CONDA_EXE=/Users/pavlo/opt/anaconda3/bin/conda
CONDA_PREFIX=/Users/pavlo/opt/anaconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/Users/pavlo/opt/anaconda3/bin/python
CONDA_ROOT=/Users/pavlo/opt/anaconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=
LD_PRELOAD=
PATH=/Users/pavlo/opt/anaconda3/bin:/Users/pavlo/opt/anaconda3/condabin:/us
r/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=

 active environment : base
active env location : /Users/pavlo/opt/anaconda3
        shell level : 1
   user config file : /Users/pavlo/.condarc

populated config files : /Users/pavlo/.condarc
conda version : 22.11.1
conda-build version : 3.21.8
python version : 3.9.12.final.0
virtual packages : __archspec=1=x86_64
__osx=10.16=0
__unix=0=0
base environment : /Users/pavlo/opt/anaconda3 (writable)
conda av data dir : /Users/pavlo/opt/anaconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/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/r/osx-64
https://conda.anaconda.org/r/noarch
https://conda.anaconda.org/anaconda/osx-64
https://conda.anaconda.org/anaconda/noarch
package cache : /Users/pavlo/opt/anaconda3/pkgs
/Users/pavlo/.conda/pkgs
envs directories : /Users/pavlo/opt/anaconda3/envs
/Users/pavlo/.conda/envs
platform : osx-64
user-agent : conda/22.11.1 requests/2.27.1 CPython/3.9.12 Darwin/21.6.0 OSX/10.16
UID:GID : 501:20
netrc file : None
offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]:
Timeout reached. No report sent.`

Then I tried to install the package just by activating all the Conda channels as suggested in the package webpage and then executing the following command:
conda install tadrep

But then I get the following error (mainly that the package cannot be found):
`Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

• tadrep

Current channels:

• https://conda.anaconda.org/conda-forge/osx-64
• https://conda.anaconda.org/conda-forge/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/r/osx-64
• https://conda.anaconda.org/r/noarch
• https://conda.anaconda.org/anaconda/osx-64
• https://conda.anaconda.org/anaconda/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.`

Then I tried with pip but then when I execute
tadrep
to see if the package was successfully installed, I get the following error:
zsh: command not found: tadrep

Could you please check if the package has been uploaded to Conda since I cannot find it on anaconda.org?

Thanks a lot for this package!

Cheers,
Pablo

[oschwengers]

Hi @pavlo888 and thanks for your interest in using TaDReP. Let me first state that this is still work in progress and neither stable nor released, so please expect changes and bugs ;-) But of course, we're very interested in early-user experiences and feedback!

This having said, the conda install tadrep will not work as there is no tadrep package on conda yet. We're sorry for the misleading readme. We're planning to release a Conda package as soon as we have a stable release. I just tested the 1st option without any issues: mamba env create --prefix ~/tmp/conda-envs/tadrep/ --file environment.yml.
Maybe an update of Conda or swith to Mamba (highly recommended) will help.

[oschwengers]

Hi @pavlo888,
FYI: TaDReP is now available via bioconda: conda install -c conda-forge -c bioconda tadrep