Editing CrocoBLAST:UserManual (section)

=1. Manage BLAST jobs=
The efficiency of CrocoBLAST lies in its ability to parallelize the execution of your BLAST jobs. This is related to breaking each big calculation into smaller pieces, and then organizing the execution of the pieces. Depending on the job, CrocoBLAST may benefit from using smaller or larger smaller pieces. CrocoBLAST automatically detects the ideal size for breaking the input file and does it for you. Alternatively, the size of each input file fragment can be manually specified in the '''GUI'''. Further, while CrocoBLAST operates with the concept of queue, it is important to note that only one job (the first on the queue) is active at any given time.

== 1.1. Creating BLAST jobs ==
{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
 |- 
 |<!--Col1-->'''a)''' Select the “Create BLAST job” tab.
 |<!--Col2-->'''b)''' Choose the desired BLAST program.
 |-
 |<!--Col1-->[[File:CrocoBLAST_addjob1.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST addjob2.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''c)''' Choose the desired database
 |<!--Col2-->'''d)''' Choose the input file that will be aligned against the database
 |-
 |<!--Col1-->[[File:CrocoBLAST_addjob3.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST addjob4.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''e)''' Choose the output folder in which the final alignment result will be created
 |<!--Col2-->'''f)''' Click on the “Add job to queue” button (note the log message below)
 |-
 |<!--Col1-->[[File:CrocoBLAST_addjob5.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST addjob6.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''g)''' That is all! Your job should now be visible on the “Manage BLAST jobs” tab
 |-
 |<!--Col1-->[[File:CrocoBLAST_addjob7.png|800x800px]]
 |}

If no "--blast_options" are specified, CrocoBLAST will use all BLAST default values.

If no "--size_of_fragment" is specified, CrocoBLAST will take up to 5 seconds to auto-detect the ideal size for that job on your computer.

When you create a BLAST job, CrocoBLAST automatically assigns each BLAST job a unique job ID, and updates the CrocoBLAST queue.

== 1.2 Removing BLAST jobs ==

In case you want to remove a BLAST job from the queue, you can follow the instructions below:

{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
 |- 
 |<!--Col1-->'''a)''' Select the “Manage BLAST jobs” tab
 |<!--Col2-->'''b)''' Select the Job you wish to remove and click the “Remove from queue” button.
 |-
 |<!--Col1-->[[File:CrocoBLAST RemoveJob1.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST RemoveJob2.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''c)''' That is it, your queue has been updated!
 |-
 |<!--Col1-->[[File:CrocoBLAST RemoveJob3.png|800x800px]]
 |}

If you wish to remove several jobs at once, you might want to use the command line example "IV.1.2.2".

== 1.3 Moving a BLAST job to the top of the queue ==

As only one job (the first on queue) is active on CrocoBLAST at each time, moving another job to the top of the queue can be useful for changing the order in which the jobs will be executed. You can move a job to the top of the CrocoBLAST queue by following the steps:

{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
 |- 
 |<!--Col1-->'''a)''' Select the “Manage BLAST jobs” tab.
 |<!--Col2-->'''b)''' Select the Job you wish to move the top of the queue.
 |-
 |<!--Col1-->[[File:CrocoBLAST Move Top1.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST Move Top2.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''c)''' That is it, your queue was updated!
 |-
 |<!--Col1-->[[File:CrocoBLAST Move Top3.png|800x800px]]
 |}