Thanks for the nice tools. I have been tinkering with it to be able to use the new versions of samtools and bcftools.
I believe this should be correct - but is depending on a proper comparison of the original output. See this issue.
Updated Monopogen to work with new versions of samtools and bcftools which are system installed through for instance conda (more generic) or brew (macOS).
Added --verbose flag to all sub-processes.
Edited mkdir and check existing tools functions.
I also created a flow to install Monopogen:
Install your favorite conda, I used miniconda3.
Create a new environment: conda create --name monopogen "python=3.8"; follow instructions (if any).
Activate the new environment: conda activate monopogen.
Make sure the monopogen-environment includes the right versions of these tools: pip install "pandas>=1.2.3" "pysam>=0.16.0.1" "NumPy>=1.19.5" "sciPy>=1.6.3" "pillow>=8.2.0"
Thanks for the nice tools. I have been tinkering with it to be able to use the new versions of
samtoolsandbcftools.I believe this should be correct - but is depending on a proper comparison of the original output. See this issue.
Monopogento work with new versions ofsamtoolsandbcftoolswhich are system installed through for instanceconda(more generic) orbrew(macOS).--verboseflag to all sub-processes.I also created a flow to install
Monopogen:conda, I usedminiconda3.conda create --name monopogen "python=3.8"; follow instructions (if any).conda activate monopogen.monopogen-environment includes the right versions of these tools:pip install "pandas>=1.2.3" "pysam>=0.16.0.1" "NumPy>=1.19.5" "sciPy>=1.6.3" "pillow>=8.2.0"