When I do the dry run, there are lots of comments about missing output files (which seems to make sense), but no clear errors. But when I run the actual command
snakemake --use-conda --configfile config.yml -j 4
I get a long error tree about r-base 3.5.1, ending with
├─ r 3.5.1 would require
│ └─ r-base >=3.5.1,<3.5.2.0a0 but there are no viable options
│ ├─ r-base 3.5.1 would require
│ │ └─ libuuid >=1.0.3,<2.0a0 , which conflicts with any installable versions previously reported;
│ └─ r-base 3.5.1 conflicts with any installable versions previously reported;
└─ r 3.5.1 conflicts with any installable versions previously reported.
r-base isn't listed in either environment.yaml or envs/SV.yml so the conda install is incomplete.
R is not installed on my system, and if I try to install it manually in the cadd.sv env , this happens:
conda install r-base=3.5.1
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 versionsThe following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.34=0
- python==3.9.9=h543edf9_0_cpython -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
- r-base=3.5.1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.34
my OS is Rocky Linux 9.1. This happened even after I installed r-base=3.5.1 in another conda env and put it in my $PATH.
I'm following the steps in README.md
When I do the dry run, there are lots of comments about missing output files (which seems to make sense), but no clear errors. But when I run the actual command
snakemake --use-conda --configfile config.yml -j 4
I get a long error tree about r-base 3.5.1, ending withr-base isn't listed in either environment.yaml or envs/SV.yml so the conda install is incomplete. R is not installed on my system, and if I try to install it manually in the
cadd.sv
env , this happens:my OS is Rocky Linux 9.1. This happened even after I installed r-base=3.5.1 in another conda env and put it in my $PATH.
What do I do next?