Comments (7)
from covid-19-signal.
This worked for me by specifying version:
conda create -c conda-forge -c bioconda -n snakemake snakemake=5.11.2 pandas
Then I get this error when running the pipeline:
Building DAG of jobs...
Creating conda environment conda_envs/ivar.yaml...
Downloading and installing remote packages.
Environment for conda_envs/ivar.yaml created (location: .snakemake/conda/1058a4d9)
Creating conda environment conda_envs/snp_mapping.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /workspace/raphenar/sars-cov-2/covid-19-sequencing/conda_envs/snp_mapping.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
ResolvePackageNotFound:
- ld_impl_linux-64==2.34=h53a641e_0
- binutils_impl_linux-64==2.34=h53a641e_0
from covid-19-signal.
I re-created the environment with python version 3.6 then I got:
Building DAG of jobs...
Creating conda environment conda_envs/trim_qc.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /workspace/raphenar/sars-cov-2/covid-19-sequencing/conda_envs/trim_qc.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
ResolvePackageNotFound:
- ld_impl_linux-64==2.34=h53a641e_0
Searching the condo channels the build number is wrong in the yaml file:
conda search ld_impl_linux-64 -c bioconda -c defaults -c conda-forge
Loading channels: done
# Name Version Build Channel
ld_impl_linux-64 2.32 5 conda-forge
ld_impl_linux-64 2.32 h53a641e_6 conda-forge
ld_impl_linux-64 2.33.1 5 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_6 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_7 pkgs/main
ld_impl_linux-64 2.33.1 h53a641e_7 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_8 conda-forge
ld_impl_linux-64 2.34 h53a641e_2 conda-forge
I will update the build number and see if this error goes away.
from covid-19-signal.
Same package with wrong build number for a different yaml file:
Building DAG of jobs...
Creating conda environment conda_envs/trim_qc.yaml...
Downloading and installing remote packages.
Environment for conda_envs/trim_qc.yaml created (location: .snakemake/conda/b49a1142)
Creating conda environment conda_envs/ivar.yaml...
Downloading and installing remote packages.
Environment for conda_envs/ivar.yaml created (location: .snakemake/conda/1058a4d9)
Creating conda environment conda_envs/assembly_qc.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /workspace/raphenar/sars-cov-2/covid-19-sequencing/conda_envs/assembly_qc.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
ResolvePackageNotFound:
- ld_impl_linux-64==2.34=h53a641e_0
@fmaguire @kmsmith137 should we not specify build numbers?
from covid-19-signal.
Updating the build (or letting conda make some decisions in which build to install) restored functionality.
from covid-19-signal.
Simplifying the env files would definitely make things easier as per 58.
from covid-19-signal.
rgi installation has had similar issues as well with versions
from covid-19-signal.
Related Issues (20)
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from covid-19-signal.