From f2ae7f02c59366b32bcc24634cbb4b6825ff4324 Mon Sep 17 00:00:00 2001
From: Kim Yang <kimy@nvidia.com>
Date: Sun, 1 Mar 2026 14:58:42 +0800
Subject: [PATCH] Enable GPU-accelerated translated search (blastx, tblastn,
 tblastx)

Pass GPU and MAKEPADDEDSEQDB_PAR variables to the translated search
workflow. When GPU is enabled and the target is nucleotide, automatically
create a padded database from the translated ORFs before the inner
protein search.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 data/workflow/translated_search.sh | 14 ++++++++++++++
 src/workflow/Search.cpp            |  2 ++
 2 files changed, 16 insertions(+)

diff --git a/data/workflow/translated_search.sh b/data/workflow/translated_search.sh
index f39c5978f..49e2f51f8 100755
--- a/data/workflow/translated_search.sh
+++ b/data/workflow/translated_search.sh
@@ -58,6 +58,14 @@ if [ -n "$NO_TARGET_INDEX" ]; then
     fi
     TARGET="${TMP_PATH}/t_orfs_aa"
     TARGET_ORF="${TMP_PATH}/t_orfs_aa"
+    if [ -n "$GPU" ]; then
+        if notExists "${TMP_PATH}/t_orfs_aa_pad.dbtype"; then
+            # shellcheck disable=SC2086
+            "$MMSEQS" makepaddedseqdb "${TMP_PATH}/t_orfs_aa" "${TMP_PATH}/t_orfs_aa_pad" ${MAKEPADDEDSEQDB_PAR} \
+                || fail "makepaddedseqdb target ORFs died"
+        fi
+        TARGET="${TMP_PATH}/t_orfs_aa_pad"
+    fi
 fi
 fi
 
@@ -96,6 +104,12 @@ if [ -n "$REMOVE_TMP" ]; then
     "$MMSEQS" rmdb "${TMP_PATH}/q_orfs_aa" ${VERBOSITY}
     # shellcheck disable=SC2086
     "$MMSEQS" rmdb "${TMP_PATH}/t_orfs_aa" ${VERBOSITY}
+    if [ -f "${TMP_PATH}/t_orfs_aa_pad.dbtype" ]; then
+        # shellcheck disable=SC2086
+        "$MMSEQS" rmdb "${TMP_PATH}/t_orfs_aa_pad" ${VERBOSITY}
+        # shellcheck disable=SC2086
+        "$MMSEQS" rmdb "${TMP_PATH}/t_orfs_aa_pad_h" ${VERBOSITY}
+    fi
     # shellcheck disable=SC2086
     "$MMSEQS" rmdb "${TMP_PATH}/aln" ${VERBOSITY}
     if [ -n "${REFERENCE_FILTER}" ]; then
diff --git a/src/workflow/Search.cpp b/src/workflow/Search.cpp
index 0e5ef3c43..7696f7802 100644
--- a/src/workflow/Search.cpp
+++ b/src/workflow/Search.cpp
@@ -588,6 +588,8 @@ int search(int argc, const char **argv, const Command& command) {
         } else {
             cmd.addVariable("ORF_PAR", par.createParameterString(par.extractorfs).c_str());
         }
+        cmd.addVariable("GPU", par.gpu ? "TRUE" : NULL);
+        cmd.addVariable("MAKEPADDEDSEQDB_PAR", par.createParameterString(par.makepaddedseqdb).c_str());
         cmd.addVariable("SEARCH", program.c_str());
         program = std::string(tmpDir + "/translated_search.sh");
         FileUtil::writeFile(program.c_str(), translated_search_sh, translated_search_sh_len);