some fixes

hooks.js

@@ -3,6 +3,12 @@
 const path = require("path");
 const { execSync } = require("child_process");
 const fs = require("fs");
+const scripts = path.join(
+  __dirname,
+  ".webpack/main/resources/biseps/workflow/scripts"
+);
+const resources = path.join(__dirname, ".webpack/main/resources/");
+const chmodr = require("chmodr");
 
 module.exports = {
   generateAssets: async (forgeConfig, options) => {
@@ -22,21 +28,34 @@ module.exports = {
     );
   },
   postStart: async (forgeConfig, options) => {
-    // chmodr(resources, 0o777, (err) => {
-    //   if (err) {
-    //     console.log("Failed to execute chmod", err);
-    //   } else {
-    //     console.log("Successful");
-    //   }
-    // });
-    // chmodr(jbrowse, 0o777, (err) => {
-    //   if (err) {
-    //     console.log("Failed to execute chmod", err);
-    //   } else {
-    //     console.log("Successful");
-    //   }
-    // });
+    chmodr(scripts, 0o777, (err) => {
+      if (err) {
+        console.log("Failed to execute chmod", err);
+      } else {
+        console.log("Successful");
+      }
+    });
+    chmodr(resources, 0o777, (err) => {
+      if (err) {
+        console.log("Failed to execute chmod", err);
+      } else {
+        console.log("Successful");
+      }
+    });
   },
 
-  postPackage: async (forgeConfig, options) => {},
+  postPackage: async (forgeConfig, options) => {
+    const resources = path.join(
+      options.outputPaths[0],
+      "resources/app/.webpack/main/resources/"
+    );
+
+    chmodr(resources, 0o777, (err) => {
+      if (err) {
+        console.log("Failed to execute chmod", err);
+      } else {
+        console.log("Successful");
+      }
+    });
+  },
 };

src/backend/snakemake.js

@@ -74,7 +74,10 @@ const spawnChild = async (body, profile, uniqueDir, homeDir, unlock) => {
             }),
             password: body.machine.password,
         };
-        if (!fs.existsSync(path.join(uniqueDir, workflow.tar.gz))) {
+        if (
+            !fs.existsSync(path.join(uniqueDir, "workflow.tar.gz")) &&
+            !body.rerun
+        ) {
             const child = exec(
                 `${command} run -n bisepsSnakemake --cwd ${uniqueDir} --no-capture-output --live-stream snakemake --profile ${profile} --config platform="other" --archive workflow.tar.gz`,
                 options

src/backend/spawnServer.js

@@ -26,7 +26,7 @@ const spawnServer = async (sock) => {
     // );
     const options = {
         slient: false,
-        detached: false,
+        detached: true,
     };
     // const child = spawn(
     //     "node",

src/components/ComparisonStepper/RunForm.js

@@ -166,6 +166,7 @@ export default function RunForm() {
     }
     const request = {
       ...compState,
+      rerun: false,
       comparisons,
       remotecomparisons,
       userId: user.user.id,

src/components/Visualization/VisualizationFill.js

@@ -18,7 +18,6 @@ import IconButton from "@material-ui/core/IconButton";
 import Container from "@material-ui/core/Container";
 
 const handler = require("serve-handler");
-const electron = window.require("electron");
 const { shell } = window.require("electron");
 const fs = require("fs");
 const http = require("http");
@@ -379,11 +378,11 @@ export default function VisualizationFill() {
             public: user.user.jbPath,
           });
         });
-
+        console.log(user.user.jbPath);
         server.listen(port[0], () => {
           console.log(server.listening);
 
-          shell.openExternal(`http:///localhost:${port[0]}`);
+          shell.openExternal(`http://localhost:${port[0]}`);
         });
         server.on("error", (err) => {
           console.log(err);