Add Vercel configuration for rewrites and build settings

99.scripts/workflow/transcripts_assembly/03.td2_cds_predict.sh

@@ -0,0 +1,18 @@
+#! /bin/bash
+set -e
+TMP=${TMP:-"$PROJECTHOME/tmp"}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <transcripts_fasta> <swissprot_database> <output_directory>"
+    echo "Predict coding sequences (CDS) from transcripts using TD2 and MMseqs2"
+    exit 1
+fi
+transcripts=$1
+sprot=$2
+outdir=$3
+
+mkdir -p "$outdir"
+TD2.LongOrfs -t "$transcripts" --precise -@ 8 -O "$outdir"
+mmseqs easy-search "$outdir/longest_orfs.pep" "$sprot" "$outdir/mmseqs.m8" "$TMP" -s 7.0 --threads 16
+TD2.Predict -t "$transcripts" --precise -O "$outdir" --retain-mmseqs-hits "$outdir/mmseqs.m8"
+echo "CDS prediction completed. Results are in $outdir"