🛠️Getting Set Up

Step 0: Requirements

COSAP currently only supports Linux-based operating systems. For other operating systems, consider using COSAP via Docker.

Mapping tasks require at least 16 GB of RAM.

Excluding annotation, data required by COSAP can take up to 50 GB in disk space.

For a typical FASTQ-processing pipeline, it is recommended that you have 3-4 times as much free disk space on your system as the size of your compressed input FASTQ files.

Step 1: Install Miniforge

COSAP requires Miniforge.

Download the script for your system and run it. For example:

bash Miniforge3-Linux-x86_64.sh

Step 2: Install COSAP

Create a Conda environment with Python 3.9 and COSAP as follows:

mamba create \
--name cosap \
--channel conda-forge \
--channel bioconda \
python=3.9 \
cosap

Then activate the environment:

mamba activate cosap

Step 3: Download Reference Files

COSAP requires the hg38 reference genome, its indexes, and several known variants sources. The following command will download files necessary for mapping and variant calling:

cosap --download-data

If you wish, you can also obtain required files yourself and place them at ~/cosap_data or the location you specified for COSAP_LIBRARY_PATH. If you wish for certain files to not be tracked by COSAP, you can specify them in a YAML file placed in the data directory:

tracked_files.yaml

ignore:
- file_1.ext
- file_2.ext

Any files previously present in the data directory will automatically be ignored when the COSAP downloader is run.

Setting up Environment Variables

Variable	Description	Default Value
COSAP_LIBRARY_PATH	Path to directory containing hg38 resources and other required data such as ENSEMBL-VEP cache.	~/cosap_data
COSAP_RAMDISK_PATH	Path to RAM disk directory.	/dev/shm
COSAP_THREADS_PER_JOB	Number of threads usable by tasks. Set to 0 or do not specify for maximum value.	All available
COSAP_IN_MEMORY_MODE	Sets run mode. If true all intermediary files will be kept in memory. Be aware that this mode increase memory consumption significantly.	False