963215de2d
- Add filter to skip .zip and .tar.gz files when creating result archive - Update CRISPR feature with CASFinder dependencies (hmmer, blast, vmatch, etc.) - Add install-casfinder task for macsydata installation - Remove obsolete CRISPR test files Co-Authored-By: Claude <noreply@anthropic.com>
31 lines
982 B
Bash
31 lines
982 B
Bash
#!/usr/bin/env bash
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set -euo pipefail
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if [[ $# -lt 2 ]]; then
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echo "Usage: $0 <input_dir> <scaf_suffix> [threads] [bttoxin_db_dir]"
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echo "Example: $0 /home/zly/project/bttoxin-pipeline/tests/test_data .fna 4"
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echo "Example with external DB: $0 /home/zly/project/bttoxin-pipeline/tests/test_data .fna 4 /home/zly/project/bttoxin-pipeline/external_dbs/bt_toxin"
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exit 1
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fi
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input_dir="$1"
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scaf_suffix="$2"
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threads="${3:-4}"
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bttoxin_db_dir="${4:-}"
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cache_dir="$(pwd)/.rattler-cache"
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mkdir -p "$cache_dir"
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if [[ -n "$bttoxin_db_dir" ]]; then
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if [[ -d "$bttoxin_db_dir" ]]; then
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env_bin="$(RATTLER_CACHE_DIR="$cache_dir" pixi run which BtToxin_Digger | xargs dirname)"
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ln -sfn "$bttoxin_db_dir" "$env_bin/BTTCMP_db/bt_toxin"
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else
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echo "[warn] bttoxin_db_dir not found: $bttoxin_db_dir" >&2
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fi
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fi
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RATTLER_CACHE_DIR="$cache_dir" pixi run BtToxin_Digger \
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--SeqPath "$input_dir" \
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--SequenceType nucl \
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--Scaf_suffix "$scaf_suffix" \
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--threads "$threads"
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