Conda-install-error

[XingnuoLi1996]

when I run "snakemake --configfile=snakemake.yml --use-conda" or "snakemake --configfile=snakemake.yml --use-conda --profile=slurm" it told me that "SyntaxError in line 920 of /public/home/GL_lixn/biosoft/dentist.v3.0.0.x86_64/Snakefile: Unexpected keyword container in rule definition (Snakefile, line 920)"

[XingnuoLi1996]

when I run "singularity shell docker://aludi/dentist:stable"

it back that

Docker image path: index.docker.io/aludi/dentist:stable Cache folder set to /public/home/GL_lixn/.singularity/docker Creating container runtime... ERROR : Failed invoking the NEWUSER namespace runtime: Invalid argument ABORT : Retval = 255

[a-ludi]

Hi, please update Snakemake to at least v5.32.1. It will solve the syntax error.

Also be aware that I will release a new version v4.0.0 of DENTIST in the coming days.

[XingnuoLi1996]

Thank you!

But when I use snakemake=v5.32.1 or other higher version snakelike to install the dentist, it back that

AttributeError in line 75 of /public/home/GL_lixn/biosoft/dentist.v3.0.0.x86_64/Snakefile: 'Workflow' object has no attribute 'sourcecache'

I'm looking forward to the release of the new version

[a-ludi]

Thanks for your feedback! Can you please tell me exactly which version of Snakemake you are using? I have neither fixed nor encountered the "sourcecache" bug, yet. I will try to fix it as soon as possible. I twill not be included in v4.0.0 though.

[XingnuoLi1996]

Hi My Conda version is 4.10.3 and python=3.6.0 snakemake=5.32.1 , snakemake=7 also back this error I hope future versions can be installed directly through Conda Thank you very much！

[a-ludi]

Hi, thank you for providing the information.

I hope future versions can be installed directly through Conda

This is already possible: conda install -c a_ludi -c bioconda dentist-core should do the trick.

[XingnuoLi1996]

Thank you! I had already install the dentist through your command: conda install -c a_ludi -c bioconda dentist-core. But I wonder that how can I execute dentist directly through Conda , you know that I can't execute it by snakemake . Now I filled the snakemake.yml . How can I execute dentist directly through Conda ? For example , dentist ---config *.yml ?

[XingnuoLi1996]

When I run snakemake --configfile=snakemake.yml --use-conda it backs: SyntaxError in line 920 of /public/home/GL_lixn/biosoft/dentist.v3.0.0.x86_64/Snakefile: Unexpected keyword container in rule definition (Snakefile, line 920)

[a-ludi]

The whole workflow for using a manually installed conda package is this:

mamba create -n dentist -c a_ludi -c bioconda dentist-core
mamba activate dentist
mamba install -c conda-forge -c bioconda snakemake
# execute your workflow; for example...
snakemake --configfile=snakemake.yml --cores=all

If you do not have mamba installed (highly recommended), then just replace it by conda. Deactivate the newly created environment with mamba deactivate.