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parklab / scan-snv

Single cell somatic genotyper
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Unable to install scan-snv #4

Open Goatofmountain opened 4 years ago

Goatofmountain commented 4 years ago

Hello, I can not install the scan-snv package on my system, and here is the error I got:

conda install -c bioconda -c conda-forge/label/cf201901 -c jluquette scansnv

Collecting package metadata: done Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  • scansnv -> eagle-phase==2.3.5=0
  • scansnv -> shapeit==2.r837=h09b0a5c_1

Current channels:

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 have tried to install the package with conda version 4.6.14, 4.7.14, 4.8.0, and 4.8.2, but it still can not be completely installed.

jluquette commented 4 years ago

Hi @Goatofmountain,

Sorry for the inconvenience. It looks like the SHAPEIT authors removed SHAPEIT v2 from bioconda and replaced it with their newest version (v4). I've rebuilt the snakemake recipe to account for this. You will also need to add -c soil -c dranew to the install command as a result. I.e.,

conda install -c bioconda -c conda-forge/label/cf201901 -c jluquette -c soil -c dranew scansnv

If you run into a segfault error during installation, a previous user worked around this by combining the conda env creation with installation with a command like:

conda create -v -n scansnvtest -c bioconda -c conda-forge/label/cf201901 -c jluquette -c soil -c dranew scansnv

Please let me know if this solves the issue for you.

Goatofmountain commented 4 years ago

I'm sorry for my delay.

Thanks for your information. My issue has been solved now. It is the second command solved my issue: conda create -v -n scansnvtest -c bioconda -c conda-forge/label/cf201901 -c jluquette -c soil -c dranew scansnv

The first command may come out with package conflicts because some packages would be installed by default when creating a new env with conda create .

Thanks again for your generous response.