Important -- This was tested with modified demic scripts version 1.0.2, please check the sourceforge.net site for any updates. One change I made was to save a couple of R data files for "manual" analysis in Rstudio if one so desires. See the git history for any other changes.
- Install sbx_coassembly from https://github.com/sunbeam-labs/sbx_coassembly
- git clone https://github.com/sunbeam-labs/sbx_demic
- cp sbx_demic $SUNBEAM_DIR/extensions/
- cat sunbeam/extensions/sbx_demic/config.yml >> sunbeam_config.yml (the config.yml that your are using for your given project)
- Edit sunbeam_config.yml to have desired parameters
- Make sure that
- all.paired_end is true if you have paired end reads
- sbx_demic.extras has any parameters you want to pass to DEMIC.pl
- sunbeam run all_demic --use-conda --configfile /path/to/config {rest of arguments for sunbeam} -- {arguments for snakemake}
See the wiki for a walkthrough of the full setup/installation and run processes.
- If you have trouble running with "--use-conda" it may be best just to install the needed packages into the sunbeam environment (e.g.
conda activate sunbeam && conda install --file sbx_demic_env.yml) and then run sunbeam in two pieces (sunbeam run all_coassemble --use-conda --configfile /path/to/config {rest of arguments for sunbeam}and thensunbeam run all_demic --configfile /path/to/config {rest of arguments for sunbeam}). Please also create a new issue on GitHub detailing the error.
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DEMIC software: https://sourceforge.net/projects/demic/files/
-
DEMIC publication: https://www.nature.com/articles/s41592-018-0182-0
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isolated Conda environment: http://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#integrated-package-management