genome diversity pipeline

To Setup:

Navigate to preferred install directory and use:

git clone https://github.com/lmrodriguezr/genome_diversity_pipeline.git

1. MiGA must be installed and available in PATH: https://manual.microbial-genomes.org/ ... On GATECH PACE server, if you have not previously done so, run: ~/shared-p/miga-conf/init.bash
2. Enveomics package must be installed and available in PATH: http://enve-omics.ce.gatech.edu/enveomics/download
3. Adjust the maximum RAM available lines 47-50 in 00_launcher.bash
4. Adjust conda module in line 8 of 00_env.bash

Conda environment installation

To Create new conda environment using conda.yml file

conda env create --prefix /path_to/shared/conda_envs -f genome_diversity_pipeline/conda.yml

conda environment should only need to be installed once per server Update shared3 and conda_env_path variable lines 21 and 22 in 00_env.bash

To add a dataset:

/path/to/pkg/01_add.bash target_dir dataset_name /path/to/reads.[12].fastq.gz

This will automatically copy and launch the pipeline step by step.

fastq files should be gzipped.

If you want to continue a halted run:

Delete the directory of the halted step ???

/path/to/pkg/xx_runme.bash target_dir dataset_name

This will detect the last complete step and lanch the next one.