Added instructions for debuuging Galaxy using a Slurm cluster

doc/source/dev/debugging_galaxy_slurm.md

@@ -14,19 +14,19 @@ playbooks for that).
 
 1. Install libslurm-dev
     * `sudo apt install libslurm-dev`
-    * On my VM, the above command puts `slurm/slurm.h` in `/usr/include` and `libslurm.a` in `/usr/lib/x86_64-linux-gnu`
+    * On my VM, the above command puts slurm/slurm.h in /usr/include and libslurm.a in /usr/lib/x86_64-linux-gnu
     * You need these header and library files to compile slurm-drmaa in the next step
 
 2. Install slurm-drmaa
-    * Download slurm-drmaa tar file from `https://github.com/natefoo/slurm-drmaa/releases/download/1.1.2/slurm-drmaa-1.1.2.tar.gz`
+    * Download slurm-drmaa tar file from https://github.com/natefoo/slurm-drmaa/releases/download/1.1.2/slurm-drmaa-1.1.2.tar.gz
     * Extract the downloaded tar file into home directory: `tar -xzvf slurm-drmaa-1.1.2.tar.gz -C ~`       
     * To compile and install slurm-drmaa
         * `cd ~/slurm-drmaa-1.1.2`
         * `./configure --with-slurm-inc=/usr/include --with-slurm-lib=/usr/lib/x86_64-linux-gpu`
         * `sudo make install`
-        * On my VM, the above command puts `libdrmaa.so` in `/usr/local/lib`. You need the path to this file in the next step
+        * On my VM, the above command puts libdrmaa.so in /usr/local/lib. You need the path to this file in the next step
 
-3. Replace the contents of `~/galaxy/config/job_conf.xml` with the following code snippet (create the file if it does not already exist)
+3. Replace the contents of ~/galaxy/config/job_conf.xml with the following code snippet (create the file if it does not already exist)
     ```
     <?xml version="1.0"?>
     <job_conf>
@@ -46,24 +46,27 @@ playbooks for that).
     </job_conf>
     ```
 
-4. Install Slurm (Instructions borrowed from `https://gist.github.com/ckandoth/2acef6310041244a690e4c08d2610423`)
+4. Uncomment the following line in ~/galaxy/config/galaxy.yml
+    * `job_config_file: job_conf.xml`
+
+5. Install Slurm (Instructions borrowed from https://gist.github.com/ckandoth/2acef6310041244a690e4c08d2610423)
     * Install the necessary packages: `sudo apt install -y slurm-wlm slurm-wlm-doc`
-    * Load `/usr/share/doc/slurm-wlm/html/configurator.html` in a browser
+    * Load /usr/share/doc/slurm-wlm/html/configurator.html in a browser
         * Set your VM's hostname in `SlurmctldHost` and `NodeName`
         * Set `StateSaveLocation` to `/var/spool/slurmctld`
         * Set `SlurmdSpoolDir` to `/var/spool/slurmd`
         * Set `ProctrackType` to `LinuxProc`
-        * Set `SelectType` to `Cons_res` 
-        * Set `SelectTypeParameters` to `CR_Core_Memory` 
+        * Set `SelectType` to `Cons_res`
+        * Set `SelectTypeParameters` to `CR_Core_Memory`
         * Set `JobAcctGatherType` to `Linux`
-        * Hit `Submit` and save the resulting text into `/etc/slurm-llnl/slurm.conf`
-            * I.e., the configuration file referred to in `/lib/systemd/system/slurmctld.service` and `/lib/systemd/system/slurmd.service`
-    * Create `/var/spool/slurmd` and `/var/spool/slurmctld` and `/var/log/slurm_jobacct.log` file and set ownership appropriately
+        * Hit Submit and save the resulting text into `/etc/slurm-llnl/slurm.conf`
+            * I.e., the configuration file referred to in /lib/systemd/system/slurmctld.service and /lib/systemd/system/slurmd.service
+    * Create /var/spool/slurmd and /var/spool/slurmctld directories and /var/log/slurm_jobacct.log file and set ownership appropriately
         * `sudo mkdir -p /var/spool/slurmd`
         * `sudo mkdir -p /var/spool/slurmctld`
         * `sudo touch /var/log/slurm_jobacct.log`
         * `sudo chown slurm:slurm /var/spool/slurmd /var/spool/slurmctld /var/log/slurm_jobacct.log`
-    * Install mailutils so that Slurm won't complain about `/bin/mail` missing
+    * Install mailutils so that Slurm won't complain about /bin/mail missing
         * `sudo apt install -y mailutils`
     * Make sure munge is installed/running, and a munge.key was created with user-only read-only permissions, owned by munge:munge
         * `sudo apt install munge`
@@ -73,6 +76,6 @@ playbooks for that).
         * `sudo service slurmd start`
         * `sudo service slurmctld start`
 
-5. Follow the instructions [here](./debuging_galaxy.md) to setup VSCode for debugging. 
+6. Follow the instructions [here](./debuging_galaxy.md) to setup VSCode for debugging. 
 
 Enjoy debugging session your Galaxy instance backed by a Slurm cluster!        

doc/source/dev/index.rst

@@ -22,5 +22,6 @@ A multi-hour long video playlist covering these slides can be found at
   writing_tests
   debugging_tests
   debugging_galaxy
+  debugging_galaxy_slurm
   starting_galaxy
   file_upload