From c1bf2c36f83bd1fdd5708795ada6c14e0f6be7e8 Mon Sep 17 00:00:00 2001
From: Skander Hatira <skander.hatira@inrae.fr>
Date: Fri, 10 Sep 2021 14:46:20 +0200
Subject: [PATCH] fixing symlink creation for adapters in remote exec
---
src/backend/helpers/createConfig.js | 6 +-----
src/backend/helpers/createSymlink.js | 14 ++++++++++----
2 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/src/backend/helpers/createConfig.js b/src/backend/helpers/createConfig.js
index 14617a2..41bc4b8 100644
--- a/src/backend/helpers/createConfig.js
+++ b/src/backend/helpers/createConfig.js
@@ -35,11 +35,7 @@ const createConfig = (body, uniqueDir) => {
},
adapters: body.remote
? path.join(".test/resources/adapters", body.adapters + ".fa")
- : path.join(
- __dirname,
- "../../resources/adapters",
- body.adapters + ".fa"
- ) || "",
+ : body.adapters,
},
params: {
diff --git a/src/backend/helpers/createSymlink.js b/src/backend/helpers/createSymlink.js
index 127dc58..d3a6439 100644
--- a/src/backend/helpers/createSymlink.js
+++ b/src/backend/helpers/createSymlink.js
@@ -15,9 +15,15 @@ const createSymlink = (body, uniqueDir) => {
body.genome,
path.join(uniqueDir, "resources/genome", path.basename(body.genome))
);
- createSymlinkSync(
- body.adapters,
- path.join(uniqueDir, "resources/adapters", path.basename(body.adapters))
- );
+ body.remote && body.customAdapters != ""
+ ? ""
+ : createSymlinkSync(
+ body.adapters,
+ path.join(
+ uniqueDir,
+ "resources/adapters",
+ path.basename(body.adapters)
+ )
+ );
};
module.exports = createSymlink;
--
GitLab