Configure ImmuneBuilder pipeline for WES execution

- Update container image to harbor.cluster.omic.ai/omic/immunebuilder:latest
- Update input/output paths to S3 (s3://omic/eureka/immunebuilder/)
- Remove local mount containerOptions (not needed in k8s)
- Update homepage to Gitea repo URL
- Clean history to remove large model weight blobs

reformat_fasta.sh

@@ -0,0 +1,70 @@
+#!/bin/bash
+# reformat_fasta.sh
+# Script to reformat RCSB FASTA files for ImmuneBuilder
+
+INPUT_DIR="/mnt/OmicNAS/private/old/olamide/ImmuneBuilder/input"
+
+# Reformat antibody FASTA (1n8z.fasta)
+# Heavy chain is typically the longer sequence, Light chain is shorter
+echo "Reformatting antibody FASTA..."
+awk '
+BEGIN { chain_count = 0; seq = "" }
+/^>/ {
+    if (seq != "") {
+        if (chain_count == 1) print ">H\n" seq
+        else if (chain_count == 2) print ">L\n" seq
+    }
+    chain_count++
+    seq = ""
+    next
+}
+{ seq = seq $0 }
+END {
+    if (chain_count == 1) print ">H\n" seq
+    else if (chain_count == 2) print ">L\n" seq
+}
+' "${INPUT_DIR}/1n8z.fasta" > "${INPUT_DIR}/1n8z_reformatted.fasta"
+
+# Reformat nanobody FASTA (3ogo_nanobody.fasta)
+# Nanobodies have only one chain (heavy)
+echo "Reformatting nanobody FASTA..."
+awk '
+BEGIN { first = 1; seq = "" }
+/^>/ {
+    if (seq != "" && first) { print ">H\n" seq; first = 0 }
+    seq = ""
+    next
+}
+{ seq = seq $0 }
+END { if (first) print ">H\n" seq }
+' "${INPUT_DIR}/3ogo_nanobody.fasta" > "${INPUT_DIR}/3ogo_nanobody_reformatted.fasta"
+
+# Reformat TCR FASTA (1oga_tcr.fasta)
+# Alpha chain first, then Beta chain
+echo "Reformatting TCR FASTA..."
+awk '
+BEGIN { chain_count = 0; seq = "" }
+/^>/ {
+    if (seq != "") {
+        if (chain_count == 1) print ">A\n" seq
+        else if (chain_count == 2) print ">B\n" seq
+    }
+    chain_count++
+    seq = ""
+    next
+}
+{ seq = seq $0 }
+END {
+    if (chain_count == 1) print ">A\n" seq
+    else if (chain_count == 2) print ">B\n" seq
+}
+' "${INPUT_DIR}/1oga_tcr.fasta" > "${INPUT_DIR}/1oga_tcr_reformatted.fasta"
+
+echo ""
+echo "Reformatted files created:"
+ls -la "${INPUT_DIR}"/*_reformatted.fasta 2>/dev/null || echo "No reformatted files found"
+echo ""
+echo "Please verify the reformatted files have correct chain labels:"
+echo "- Antibody: >H and >L"
+echo "- Nanobody: >H only"
+echo "- TCR: >A and >B"