Initial commit

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

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+#!/bin/bash
+# run_compleasm_parallel.sh
+source ~/.bashrc
+conda activate phylo
+
+# Threading configuration (adjust based on your system)
+TOTAL_THREADS=TOTAL_THREADS      # Total cores to use (e.g., 64)
+THREADS_PER_JOB=THREADS_PER_JOB  # Threads per genome (e.g., 16)
+CONCURRENT_JOBS=$((TOTAL_THREADS / THREADS_PER_JOB))  # Calculated automatically
+
+echo "Configuration:"
+echo "  Total threads:      ${TOTAL_THREADS}"
+echo "  Threads per genome: ${THREADS_PER_JOB}"
+echo "  Concurrent genomes: ${CONCURRENT_JOBS}"
+echo ""
+
+# Create output directory
+mkdir -p 01_busco_results
+
+# Process remaining genomes (skip first one) in parallel
+tail -n +2 genome_list.txt | parallel -j ${CONCURRENT_JOBS} '
+  genome_name=$(basename {} .fasta)
+  echo "Processing ${genome_name} with THREADS_PER_JOB threads..."
+
+  compleasm run \
+    -a {} \
+    -o 01_busco_results/${genome_name}_compleasm \
+    -l LINEAGE \
+    -t THREADS_PER_JOB
+'
+
+echo ""
+echo "All genomes processed!"