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configuration-files.md

@@ -118,7 +118,7 @@ This is a drop down menu where you will select one of the following:
 This designates the job to be completed locally.
 * *Sq_Sub*  
 This designates the job to be completed on the Sharcnet.  
-  * Other schedulers are currently being developed including qSub.   
+  * Other schedulers are currently being developed including qSub and Slurm.  
 :b: The default depends on whether you loaded the local or remote file.
 
 **2. Replace String**  
@@ -128,10 +128,10 @@ This designates the job to be completed on the Sharcnet.
 
  ***   
   
-To find out which variables the config file must setas swap strings, look in the comments at the top of the scripts.
+To find out which variables the config file must set as swap strings, look in the comments at the top of the scripts.
   ![swpstrpart2](/uploads/5d92049f629fcc35bdcbbdf2a4193fa1/swpstrpart2.png)  
-Swap string is also helpful as you can change variables like filtered frequencies by simply editing the text config files, rather then changing the script code.
- * **[batch_dfn] and [batch_dfp] []**  are special swap strings that are not collected from the config file. Instead it is the name of the current data file and the current script.
+Swap string is also helpful as you can change variables like filtered frequencies by simply editing the text config files, rather then changing the script code. You can also use them to make decisions on options like 'yes' or 'no' to preform different sections of code within the script.
+ * **[batch_dfn] and [batch_dfp] **  are special swap strings that are not collected from the config file. Instead they are gathered from the loaded EEG data files.
 
 **3. Order**  
 * The order of the script is an important part of creating a script pipeline. If you leave this section empty your scripts will be run in a default linear order same as the local job order.When running a job locally your computer will focus on one task at a time so your script order will be:  
@@ -148,17 +148,18 @@ In the example below the first script is number [1]. After it is complete both s
 
 **4. Job Name**  
 * This will indicate what the job name will be. Batch swap string rules apply.  
-:b: Default as *[batch_hfn,.,1]_[batch_dfn,.,1]* indicating that the job name will be named after the current script followed by the subject file number.
+:b: Default as *[batch_hfn,.,1]_[batch_dfn,.,1]* indicating that the job name will be named after the current script followed by the the name of the data file.
   
 **5. Session Init**  
 * This field will contain the location of any scripts you need to run on the remote sever at the beginning of the session. If you are running a project locally you can leave this field blank.    
-:b: Remote Default for Octave is *analysis/support/config/octave.sesinit* containing:
+:b: Remote Default for Octave is *analysis/support/config/octave.sesinit* containing a few lines to unload and load the correct version of Octave.
 
 ```  
 module unload intel/12.1.3;
 module unload octave;
 module load octave/3.8.1;
 ```
+If you are running a different program other than octave your session init scrip will be different. The tutorial also contains a session init file for AMICA.  
 
 **6. Job Init**  
 * This field will contain the location of any scripts you need to run on the remote sever at the beginning of the job. If you are running a project locally you can leave this field blank.   
@@ -174,10 +175,14 @@ pkg load signal;
 addpath(genpath('[:,1,remote_dependency]'));
 cd '[:,1,remote_project_work]';
 ```
+It also contains a loop which will remove the *Fieldtrip* plugin as it will crash Octave.  
 
 **8. Scheduler Options**  
 * This section contains a series of characters to communicate the job specifications to the remote server, such as memory and time. Click on the field and look at the information box below to see the specific commands. If you are running a project locally you can leave this field blank.   
 :b: Remote default is *-r 4h --mpp 6G*  for Octave Scripts and *-r 4h -q -mpi 1G* for amica files.
+These should be adjusted based on what server you are running your jobs on as well as the kind of process you are preforming. Some jobs will require more time and some will require more memory. These also effect the que time your jobs will have in the scheduler. Most of the time jobs with shorter time and lower memory will get into que faster, but you also don't want your job to crash as you did not give it enough resources.    
+
+The nature of the string also depends on what scheduler you are using. The current systems use qsub or sqsub, but as of April 2017 the new Sharcnet servers will be using Slurm.  
 
 **9. Software**  
 This is a drop down menu where you can select one of the following: