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fix issue with java path #207

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Merged
madhavajay merged 1 commit into from
Feb 23, 2026
Merged

fix issue with java path #207

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16 changes: 13 additions & 3 deletions repo
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Original file line number Diff line number Diff line change
Expand Up @@ -566,9 +566,19 @@ ensure_syqure_submodules() {

echo -e "${CYAN}→ ${repo} submodules${NC}"
git -C "$repo" submodule sync --recursive >/dev/null 2>&1 || true
if ! git -C "$repo" submodule update --init --recursive --depth 1; then
echo -e "${YELLOW}WARN: ${repo} shallow submodule update failed; retrying full depth${NC}"
if ! git -C "$repo" submodule update --init --recursive; then
git -C "$repo" config submodule.external/llvm-project.shallow true >/dev/null 2>&1 || true
git -C "$repo" config submodule.external/llvm-project.partialClone true >/dev/null 2>&1 || true
git -C "$repo" config submodule.external/llvm-project.partialCloneFilter blob:none >/dev/null 2>&1 || true

# Keep llvm-project shallow because it is large.
if ! git -C "$repo" submodule update --init --depth 1 --filter=blob:none -- external/llvm-project; then
echo -e "${RED}✗ ${repo} llvm-project shallow submodule update failed${NC}" >&2
return 1
fi

if ! git -C "$repo" submodule update --init --recursive --depth 1 -- codon sequre; then
echo -e "${YELLOW}WARN: ${repo} shallow codon/sequre update failed; retrying full depth${NC}"
if ! git -C "$repo" submodule update --init --recursive -- codon sequre; then
echo -e "${RED}✗ ${repo} submodule update failed${NC}" >&2
return 1
fi
Expand Down
2 changes: 1 addition & 1 deletion src-tauri/Cargo.lock
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35 changes: 35 additions & 0 deletions src-tauri/src/commands/runs.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -257,6 +257,7 @@ pub async fn execute_analysis(
// Capture original environment for logging
let original_path = env::var("PATH").unwrap_or_default();
let original_java_home = env::var("JAVA_HOME").ok();
let original_java_cmd = env::var("JAVA_CMD").ok();

let mut env_lines = vec![
"=== Nextflow environment ===".to_string(),
Expand All @@ -279,6 +280,12 @@ pub async fn execute_analysis(
.clone()
.unwrap_or_else(|| "<unset>".to_string())
),
format!(
" JAVA_CMD (original) = {}",
original_java_cmd
.clone()
.unwrap_or_else(|| "<unset>".to_string())
),
];

let config = match biovault::config::get_config() {
Expand Down Expand Up @@ -319,8 +326,12 @@ pub async fn execute_analysis(
}

let mut java_home_set = false;
let mut java_cmd_set = false;
if let Some(java_bin) = resolve_binary_path(config.as_ref(), "java") {
env_lines.push(format!(" java binary = {}", java_bin));
env::set_var("JAVA_CMD", &java_bin);
env_lines.push(format!(" JAVA_CMD set from java binary = {}", java_bin));
java_cmd_set = true;
if let Some(java_home) = derive_java_home(&java_bin) {
env::set_var("JAVA_HOME", &java_home);
env_lines.push(format!(
Expand All @@ -345,6 +356,26 @@ pub async fn execute_analysis(
}
}

if !java_cmd_set {
match original_java_cmd.as_deref() {
Some(existing) => {
if std::path::Path::new(existing).exists() {
env_lines.push(format!(" JAVA_CMD retained (pre-existing) = {}", existing));
} else {
env::remove_var("JAVA_CMD");
env_lines.push(format!(
" JAVA_CMD removed (pre-existing path missing) = {}",
existing
));
}
}
None => {
env::remove_var("JAVA_CMD");
env_lines.push(" JAVA_CMD (effective) = <unset>".to_string());
}
}
}

let nxf_home_path = biovault_home.join("data").join("nextflow");
match fs::create_dir_all(&nxf_home_path) {
Ok(_) => {
Expand All @@ -366,6 +397,10 @@ pub async fn execute_analysis(
" JAVA_HOME (effective) = {}",
env::var("JAVA_HOME").unwrap_or_else(|_| "<unset>".to_string())
));
env_lines.push(format!(
" JAVA_CMD (effective) = {}",
env::var("JAVA_CMD").unwrap_or_else(|_| "<unset>".to_string())
));
env_lines.push(format!(
" NXF_HOME (effective) = {}",
env::var("NXF_HOME").unwrap_or_else(|_| "<unset>".to_string())
Expand Down
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