having the same issue, couldn't find a working solution yet. here are the solutions I have tried:
installation with conda install charger command:
First, I configured bioconda channel as specified in README using following command:
conda config --add channels bioconda
gave me this output:
Loading channels: done
No match found for: charger. Search: *charger*
PackagesNotFoundError: The following packages are not available from current channels:
- charger
Current channels:
- https://conda.anaconda.org/conda-forge/linux-64
- https://conda.anaconda.org/conda-forge/noarch
- https://conda.anaconda.org/bioconda/linux-64
- https://conda.anaconda.org/bioconda/noarch
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-64
- https://repo.anaconda.com/pkgs/r/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.
I searched for "charger" package in the Anaconda library. I couldn't find anything related. Which means package really doesn't exist in Anaconda library.
installation with pip install charger command:
There is a warning in README which says "CharGer requires Python 3.6+.". To prevent package conflicts, i created a virtual environment. Then activated the virtual environment with following command:
zeynep@genomics1:~/files/charger$ source charger/bin/activate
verification of Python version is newer than 3.6+:
(charger) zeynep@genomics1:~/files/charger$ which python /home/zeynep/files/charger/charger/bin/python (charger) zeynep@genomics1:~/files/charger$ /home/zeynep/files/charger/charger/bin/python --version Python 3.10.12
When I type charger -h it gives me following error:
File "/home/zeynep/files/charger/charger/bin/charger", line 256 print "CharGer ERROR: Command not recognized" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(...)?
When I searched for the reason of this error, what I found is it's due to syntax update after Python 2.7. So, in README it says CharGer requires Python 3.6+ but now I got this syntax error caused by not using Python 2.7.
Then i created a conda environment with Python 2.7 and activated it:
For Python 2.7 you need to manually install pip:
curl https://bootstrap.pypa.io/pip/2.7/get-pip.py -o get-pip.py python get-pip.py --force-reinstall
Then i tried installing CharGer with Python 2.7 and it worked.
You need to remove conda install option in README to prevent misinformation.
Other than that, how can I use Python 3.6+ with charger as written in README instead of Python 2.7?
having the same issue, couldn't find a working solution yet. here are the solutions I have tried:
conda install chargercommand:First, I configured bioconda channel as specified in README using following command:
conda config --add channels biocondagave me this output:pip install chargercommand:There is a warning in README which says "CharGer requires Python 3.6+.". To prevent package conflicts, i created a virtual environment. Then activated the virtual environment with following command:
zeynep@genomics1:~/files/charger$ source charger/bin/activateverification of Python version is newer than 3.6+:
(charger) zeynep@genomics1:~/files/charger$ which python /home/zeynep/files/charger/charger/bin/python (charger) zeynep@genomics1:~/files/charger$ /home/zeynep/files/charger/charger/bin/python --version Python 3.10.12When I type
charger -hit gives me following error:File "/home/zeynep/files/charger/charger/bin/charger", line 256 print "CharGer ERROR: Command not recognized" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(...)?When I searched for the reason of this error, what I found is it's due to syntax update after Python 2.7. So, in README it says CharGer requires Python 3.6+ but now I got this syntax error caused by not using Python 2.7.
Then i created a conda environment with Python 2.7 and activated it:
conda create --name py27 python=2.7 conda activate py27For Python 2.7 you need to manually install pip:
curl https://bootstrap.pypa.io/pip/2.7/get-pip.py -o get-pip.py python get-pip.py --force-reinstallThen i tried installing CharGer with Python 2.7 and it worked.
You need to remove conda install option in README to prevent misinformation. Other than that, how can I use Python 3.6+ with charger as written in README instead of Python 2.7?
Thank you!