When trying to connect Cell Ranger to the conda environment as described in the README, an error might occur similar to this one:
ln: failed to create symbolic link '/software/python-anaconda-2022.05-el8-x86_64/envs/snakemake8/bin/cellranger': No such file or directory
Apparently, this error is caused by a mismatch between conda info --base and the actual location in which the conda environment is installed, such as in the example below:
$ conda info --base
/software/python-anaconda-2022.05-el8-x86_64
$ conda env list | head
snakemake8 * /home/daraujo/.conda/envs/snakemake8
base /software/python-anaconda-2022.05-el8-x86_64
R /software/python-anaconda-2022.05-el8-x86_64/envs/R
Thus, to fix this issue, use the proper conda environment path instead of $(conda info --base). This should correctly connect Cell Ranger to the conda environment.
When trying to connect Cell Ranger to the conda environment as described in the README, an error might occur similar to this one:
ln: failed to create symbolic link '/software/python-anaconda-2022.05-el8-x86_64/envs/snakemake8/bin/cellranger': No such file or directoryApparently, this error is caused by a mismatch between
conda info --baseand the actual location in which the conda environment is installed, such as in the example below:Thus, to fix this issue, use the proper conda environment path instead of
$(conda info --base). This should correctly connect Cell Ranger to the conda environment.