TemperatureDependentCelegansAging_Spang.template.env

# ==========================================
# CRISPR Projects - Environment Template
# ==========================================
# INSTRUCTIONS:
# 1. Copy this file and rename it to your local environment (e.g. in our case we specify paths on scicore HPC cluster and name it TemperatureDependentCelegansAging_Spang.scicore.env).
# 2. Replace the placeholder paths in the "Base Directories" section with your actual paths.
# 3. DO NOT commit your actual personalized .env file to version control.

# --- Base Directories (USER MUST MODIFY THESE) ---
LAB_GROUP_DIR=/path/to/your/shared/group/folder/
MAIN_PROJECT_DIR=/path/to/your/shared/group/TemperatureDependentCelegansAging_Spang/
WF_DIR=/path/to/your/local/Projects/TemperatureDependentCelegansAging_Spang/WF/
UCSC_TRACKS_DIR=/path/to/your/shared/ucsc_tracks/
CELEGANS_ANNOTATION_DIR=/path/to/your/shared/Genomes/c_elegans/

# =========================================================================
# THE PATHS BELOW ARE AUTO-GENERATED BASED ON THE BASE DIRECTORIES ABOVE.
# ONLY MODIFY THESE IF YOU ARE CHANGING THE CORE PROJECT STRUCTURE.
# =========================================================================

# --- UCSC Subdirectories ---
UCSC_TRACKFILES_DIR=${UCSC_TRACKS_DIR}trackfiles/
UCSC_TRACKHUBS_DIR=${UCSC_TRACKS_DIR}trackhubs/

# --- Shared Project Subdirectories ---
SHARED_PROJECT_DIR=${MAIN_PROJECT_DIR}
TEMP_DIR=${SHARED_PROJECT_DIR}temp_dir/
SLURM_DIR=${TEMP_DIR}slurm/
SLURM_SCRIPTS_DIR=${SHARED_PROJECT_DIR}scripts/
FIGURES_DIR=${SHARED_PROJECT_DIR}figures/
TABLES_DIR=${SHARED_PROJECT_DIR}tables/
FASTQ_DIR=${SHARED_PROJECT_DIR}input_fastq/
METADATA_DIR=${SHARED_PROJECT_DIR}metadata/
WF_RUNS_DIR=${SHARED_PROJECT_DIR}wf_runs/
CONFIGS_DIR=${SHARED_PROJECT_DIR}configs/ # where to store the filled-in .env file

# --- Genome Annotation Files ---
CELEGANS_GENOME_FILE=${CELEGANS_ANNOTATION_DIR}GRCh38.primary_assembly.genome.fa
CELEGANS_CHROM_SIZES_FILE=${CELEGANS_ANNOTATION_DIR}hg38.chrom.sizes
CELEGANS_ANNOTATION_FILE=${CELEGANS_ANNOTATION_DIR}hg38_v42/gencode.v42.annotation.gtf
CELEGANS_BASIC_ANNOTATION_FILE=${CELEGANS_ANNOTATION_DIR}hg38_v42/gencode.v42.basic.annotation.gtf
CELEGANS_POLYASITE_ATLAS=${CELEGANS_ANNOTATION_DIR}/atlas.clusters.3.0.GRCh38.GENCODE_42.bed.gz