I feel like it must be something really simple but i just cant get the pipeline to install, its either conflicting dependencies messages or errors such as these below. Sorry to bother!
CONDA Install error
(base) C:\Users\marcy>conda install -c bioconda artic
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
'.' is not recognized as an internal or external command,
operable program or batch file.
'.' is not recognized as an internal or external command,
operable program or batch file.
pysam: htslib configure options: None
error: [WinError 2] The system cannot find the file specified
I feel like it must be something really simple but i just cant get the pipeline to install, its either conflicting dependencies messages or errors such as these below. Sorry to bother!
CONDA Install error (base) C:\Users\marcy>conda install -c bioconda artic Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
error from source when installing pysam
Installed c:\users\marcy\miniconda3\lib\site-packages\artic-1.2.1-py3.8.egg Processing dependencies for artic==1.2.1 Searching for pysam Reading https://pypi.org/simple/pysam/ Downloading https://files.pythonhosted.org/packages/99/5a/fc440eb5fffb5346e61a38b49991aa552e4b8b31e8493a101d2833ed1e19/pysam-0.16.0.1.tar.gz#sha256=d428a9768691d5ea3c28cc52a949c920ae691aa4c110a8b7328dc4d165ef1ad6 Best match: pysam 0.16.0.1 Processing pysam-0.16.0.1.tar.gz Writing C:\Users\marcy\AppData\Local\Temp\easyinstall-4f2jrqf\pysam-0.16.0.1\setup.cfg Running pysam-0.16.0.1\setup.py -q bdist_egg --dist-dir C:\Users\marcy\AppData\Local\Temp\easyinstall-4f2jrqf\pysam-0.16.0.1\egg-dist-tmp-qwc20qzo
pysam: no cython available - using pre-compiled C
pysam: htslib mode is shared
pysam: HTSLIB_CONFIGURE_OPTIONS=None
'.' is not recognized as an internal or external command, operable program or batch file. '.' is not recognized as an internal or external command, operable program or batch file.
pysam: htslib configure options: None
error: [WinError 2] The system cannot find the file specified