/sbx_demic

A sunbeam extension to run DEMIC, a peak-to-trough ratio generator for bacteria short-reads

Primary LanguagePerlGNU General Public License v3.0GPL-3.0

sbx_demic

Sunbeam extension for DEMIC

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.

Installation

  1. Install sbx_coassembly from https://github.com/sunbeam-labs/sbx_coassembly
  2. git clone https://github.com/sunbeam-labs/sbx_demic
  3. cp sbx_demic $SUNBEAM_DIR/extensions/
  4. cat sunbeam/extensions/sbx_demic/config.yml >> sunbeam_config.yml (the config.yml that your are using for your given project)
  5. 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

Running

  1. 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.

Trouble-shooting

  • 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 then sunbeam run all_demic --configfile /path/to/config {rest of arguments for sunbeam}). Please also create a new issue on GitHub detailing the error.

References