Closed jessieolough closed 7 months ago
smcolby
commented
7 months ago Hi Jessie,
After investigating this further, it appears snakemake has made significant changes with version 8.*. I'll keep this issue open as a reminder to update deimos to reflect the version 8 API changes, but for now please install version 7.*.
mamba/conda install -c bioconda snakemake=7
jessieolough
commented
7 months ago Hi smcolby,
Thanks for your response. When I used conda install -c bioconda snakemake=7 I got the following error:
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: unsuccessful initial attempt using 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 versionsI alternatively tried just using pip install snakemake==7, but I then got this error message instead:
Collecting snakemake==7
Downloading snakemake-7.0.0.tar.gz (286 kB)
---------------------------------------- 286.1/286.1 kB 8.9 MB/s eta 0:00:00
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [18 lines of output]
C:\Users\jessieolough\AppData\Local\Temp\2\pip-install-gklk51zb\snakemake_88c530f12ed54f40868ba452555c0d46\versioneer.py:421: SyntaxWarning: invalid escape sequence '\s'
LONG_VERSION_PY['git'] = '''
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "C:\Users\jessieolough\AppData\Local\Temp\2\pip-install-gklk51zb\snakemake_88c530f12ed54f40868ba452555c0d46\setup.py", line 28, in <module>
version=versioneer.get_version(),
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\jessieolough\AppData\Local\Temp\2\pip-install-gklk51zb\snakemake_88c530f12ed54f40868ba452555c0d46\versioneer.py", line 1480, in get_version
return get_versions()["version"]
^^^^^^^^^^^^^^
File "C:\Users\jessieolough\AppData\Local\Temp\2\pip-install-gklk51zb\snakemake_88c530f12ed54f40868ba452555c0d46\versioneer.py", line 1412, in get_versions
cfg = get_config_from_root(root)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\jessieolough\AppData\Local\Temp\2\pip-install-gklk51zb\snakemake_88c530f12ed54f40868ba452555c0d46\versioneer.py", line 342, in get_config_from_root
parser = configparser.SafeConfigParser()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.I followed advice with a modified pip install snakemake==7 --use-deprecated=legacy-resolver command, which resulted in this error:
Collecting snakemake==7
Using cached snakemake-7.0.0.tar.gz (286 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [18 lines of output]
C:\Users\jessieolough\AppData\Local\Temp\2\pip-install-tq4ola64\snakemake\versioneer.py:421: SyntaxWarning: invalid escape sequence '\s'
LONG_VERSION_PY['git'] = '''
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "C:\Users\jessieolough\AppData\Local\Temp\2\pip-install-tq4ola64\snakemake\setup.py", line 28, in <module>
version=versioneer.get_version(),
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\jessieolough\AppData\Local\Temp\2\pip-install-tq4ola64\snakemake\versioneer.py", line 1480, in get_version
return get_versions()["version"]
^^^^^^^^^^^^^^
File "C:\Users\jessieolough\AppData\Local\Temp\2\pip-install-tq4ola64\snakemake\versioneer.py", line 1412, in get_versions
cfg = get_config_from_root(root)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\jessieolough\AppData\Local\Temp\2\pip-install-tq4ola64\snakemake\versioneer.py", line 342, in get_config_from_root
parser = configparser.SafeConfigParser()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> snakemake
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.Other sources suggest to do it again in a new environment, though this environment is already quite new and I am unsure whether this will work.
Any further suggestions would be much appreciated.
Many thanks, Jess
smcolby
commented
7 months ago What a headache! I just pushed a branch that specifies snakemake version less than 8. It's running through tests now. If it passes against Windows, I'll merge and you should then be able to install a fresh environment from environment.yml.
smcolby
commented
7 months ago Okay, pull request passed tests on all platforms. Please give a fresh environment install a shot and let me know how it goes!
jessieolough
commented
7 months ago Success! I reinstalled the deimos environment again and I now get the expected output using deimos -h in the command line.
Thanks so much for all your help!
smcolby
commented
7 months ago Excellent!
Hello,
I have recently installed DEIMoS on my Windows 10 PC. However, when I use the
deimos -hcommand I get the following error message:From the
pip freezeoutput from the deimos conda environment (below), it looks as though snakemake is already present. The environment is using Python 3.12.2.I am unsure how else to deal with this issue and any help with this issue would be much appreciated.
Many thanks, jessieolough