Initial commit

skills/phylo_from_buscos/templates/local/02_compleasm_first.sh

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+#!/bin/bash
+# run_compleasm_first.sh
+source ~/.bashrc
+conda activate phylo
+
+# User-specified total CPU threads
+TOTAL_THREADS=TOTAL_THREADS  # Replace with total cores you want to use (e.g., 16, 32, 64)
+echo "Processing first genome with ${TOTAL_THREADS} CPU threads to download lineage database..."
+
+# Create output directory
+mkdir -p 01_busco_results
+
+# Process FIRST genome only
+first_genome=$(head -n 1 genome_list.txt)
+genome_name=$(basename ${first_genome} .fasta)
+echo "Processing: ${genome_name}"
+
+compleasm run \
+  -a ${first_genome} \
+  -o 01_busco_results/${genome_name}_compleasm \
+  -l LINEAGE \
+  -t ${TOTAL_THREADS}
+
+echo ""
+echo "First genome complete! Lineage database is now cached."
+echo "Now run the parallel script for remaining genomes: bash run_compleasm_parallel.sh"