I have just started using miniconda on windows and was creating an environment through a .yml file but got this error.
C:\WINDOWS\system32>conda env create -f crispr-env.yml
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "F:\miniana\lib\site-packages\conda\exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "F:\miniana\lib\site-packages\conda_env\cli\main.py", line 80, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "F:\miniana\lib\site-packages\conda_env\cli\main_create.py", line 79, in execute
spec = specs.detect(name=name, filename=expand(args.file),
File "F:\miniana\lib\site-packages\conda_env\specs\__init__.py", line 40, in detect
if spec.can_handle():
File "F:\miniana\lib\site-packages\conda_env\specs\yaml_file.py", line 18, in can_handle
self._environment = env.from_file(self.filename)
File "F:\miniana\lib\site-packages\conda_env\env.py", line 151, in from_file
return from_yaml(yamlstr, filename=filename)
File "F:\miniana\lib\site-packages\conda_env\env.py", line 137, in from_yaml
data = validate_keys(data, kwargs)
File "F:\miniana\lib\site-packages\conda_env\env.py", line 36, in validate_keys
for key in data.keys():
AttributeError: 'NoneType' object has no attribute 'keys'
environment variables:
CIO_TEST=<not set>
CONDA_AUTO_UPDATE_CONDA=false
CONDA_EXE=F:\miniana\condabin\..\Scripts\conda.exe
CONDA_EXES="F:\miniana\condabin\..\Scripts\conda.exe"
CONDA_ROOT=F:\miniana
HOMEPATH=\Users\Aakash Yadav
PATH=F:\miniana;F:\miniana\Library\mingw-w64\bin;F:\miniana\Library\usr\bin
;F:\miniana\Library\bin;F:\miniana\Scripts;F:\miniana\bin;C:\Program
Files (x86)\NVIDIA Corporation\PhysX\Common;C:\ProgramData\Oracle\Java
\javapath;C:\Program Files (x86)\Intel\iCLS Client\;C:\Program
Files\Intel\iCLS Client\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\Sys
tem32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;c:\Program
Files\Intel\WiFi\bin\;c:\Program Files\Common
Files\Intel\WirelessCommon\;C:\Program Files (x86)\Intel\Intel(R)
Management Engine Components\DAL;C:\Program Files\Intel\Intel(R)
Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R)
Management Engine Components\IPT;C:\Program Files\Intel\Intel(R)
Management Engine Components\IPT;C:\Program Files\Microsoft Windows
Performance Toolkit\;C:\TDM-GCC-64\bin;C:\Program
Files\Git\cmd;C:\Program Files\Java\jdk1.8.0_112\bin;C:\Users\Aakash
Yadav\AppData\Local\Microsoft\WindowsApps;C:\Program Files (x86)\Googl
e\Chrome\Application;F:\miniana\condabin;F:\miniana\pkgs;F:\miniana;F:
\miniana\Library\bin;F:\miniana\Scripts;F:\pilercr1.06
PSMODULEPATH=C:\WINDOWS\system32\WindowsPowerShell\v1.0\Modules\
RASMOLPATH=C:\Program Files (x86)\RasWin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
VBOX_MSI_INSTALL_PATH=C:\Program Files\Oracle\VirtualBox\
active environment : None
user config file : C:\Users\Aakash Yadav\.condarc
populated config files : C:\Users\Aakash Yadav\.condarc
conda version : 4.8.3
conda-build version : not installed
python version : 3.8.3.final.0
virtual packages :
base environment : F:\miniana (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/win-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/msys2/win-64
https://repo.anaconda.com/pkgs/msys2/noarch
package cache : F:\miniana\pkgs
C:\Users\Aakash Yadav\.conda\pkgs
C:\Users\Aakash Yadav\AppData\Local\conda\conda\pkgs
envs directories : F:\miniana\envs
C:\Users\Aakash Yadav\.conda\envs
C:\Users\Aakash Yadav\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/4.8.3 requests/2.24.0 CPython/3.8.3 Windows/10 Windows/10.0.14393
administrator : True
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
crispr-env.yml:
name: crispr-env
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=main
- blas=1.0=openblas
- ca-certificates=2020.4.5.1=hecc5488_0
- certifi=2020.4.5.1=py37hc8dfbb8_0
- hmmer=3.2.1=he1b5a44_2
- joblib=0.14.1=py_0
- ld_impl_linux-64=2.33.1=h53a641e_7
- libedit=3.1.20181209=hc058e9b_0
- libffi=3.2.1=hd88cf55_4
- libgcc-ng=9.1.0=hdf63c60_0
- libgfortran-ng=7.3.0=hdf63c60_0
- libopenblas=0.3.6=h5a2b251_2
- libstdcxx-ng=9.1.0=hdf63c60_0
- ncurses=6.2=he6710b0_0
- nomkl=3.0=0
- numpy=1.17.4=py37hd5be1e1_0
- numpy-base=1.17.4=py37h2f8d375_0
- openssl=1.1.1f=h516909a_0
- pandas=0.25.3=py37he6710b0_0
- pip=20.0.2=py37_1
- prodigal=2.6.3=h516909a_2
- python=3.7.6=h0371630_2
- python-dateutil=2.8.1=py_0
- python_abi=3.7=1_cp37m
- pytz=2019.3=py_0
- readline=7.0=h7b6447c_5
- scikit-learn=0.22.1=py37h22eb022_0
- scipy=1.3.2=py37he2b7bc3_0
- setuptools=46.1.3=py37_0
- six=1.14.0=py37_0
- sqlite=3.31.1=h7b6447c_0
- tk=8.6.8=hbc83047_0
- wheel=0.34.2=py37_0
- xz=5.2.4=h14c3975_4
- zlib=1.2.11=h7b6447c_3
i changed the dir. and the command and i am getting this error:
C:\Windows\System32\CRISPRcasIdentifier>conda env create -f crispr-env.yml -n crispr-env
Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound:
- zlib==1.2.11=h7b6447c_3
- libgfortran-ng==7.3.0=hdf63c60_0
- libopenblas==0.3.6=h5a2b251_2
- tk==8.6.8=hbc83047_0
- openssl==1.1.1f=h516909a_0
- scikit-learn==0.22.1=py37h22eb022_0
- ld_impl_linux-64==2.33.1=h53a641e_7
- readline==7.0=h7b6447c_5
- xz==5.2.4=h14c3975_4
- numpy==1.17.4=py37hd5be1e1_0
- sqlite==3.31.1=h7b6447c_0
- numpy-base==1.17.4=py37h2f8d375_0
- prodigal==2.6.3=h516909a_2
- libstdcxx-ng==9.1.0=hdf63c60_0
- pandas==0.25.3=py37he6710b0_0
- scipy==1.3.2=py37he2b7bc3_0
- nomkl==3.0=0
- libgcc-ng==9.1.0=hdf63c60_0
- hmmer==3.2.1=he1b5a44_2
- libedit==3.1.20181209=hc058e9b_0
- python==3.7.6=h0371630_2
- ncurses==6.2=he6710b0_0
- libffi==3.2.1=hd88cf55_4
Should i delete these dependencies or is there another way to solve this package error?
There are a couple of issues. First, going across platforms (linux-64 to win-64) is not directly supported. There are other answers that address this. Second, and more prohibitive, is that Bioconda does not support Windows and some of the packages (e.g., hmmer) are specifically from there.
Alternatives could be either building up the dependencies in Conda env, plus a compiler meta-package (compiler-cxx, make), then installing non-Windows software from source (e.g., see HMMER documentation); or running Conda under WSL.