Differences

This shows you the differences between two versions of the page.

--- mkatari-bioinformatics-august-2013-blastnotes [2013/08/13 15:28] – mkatari
+++ mkatari-bioinformatics-august-2013-blastnotes [2013/08/13 15:29] – mkatari
@@ Line 1: / Line 1: @@
 ====== Run Blast using sbatch ======
-  - Create a new sbatch file (call it ''contigs.fa.nr.sbatch'') with the following heading. The ''#!'' MUST be the first line of the file. This tells the computer (or in this case snatch) to run the code using the ''bash'' shell interpreter.
+  * Create a new sbatch file (call it ''contigs.fa.nr.sbatch'') with the following heading. The ''#!'' MUST be the first line of the file. This tells the computer (or in this case snatch) to run the code using the ''bash'' shell interpreter.
 <code>
@@ Line 12: / Line 12: @@
 Normally any other ''#'' used in a bash script file means a comment follows. However since we are executing the sbatch file using sbatch command (see below) SBATCH knows to look for ''#SBATCH'' and use the information that follows. Here we are telling the SBATCH file to use the ''highmem'' partition (the mammoth server) and use ''8'' CPUs to perform the calculation. It is also important to tell that program you are running that it has 8 CPUs available so it will use them, else you will be reserving 8 CPUs but only using one.
-  - There are several different job managers and different ways of setting up HPC computer systems. In practice I prefer not to assume that a job that is submitted to a different server will know how to find the different commands or even files. So I like to include the full paths for both. In order to find where the ''blastx'' command is located I simply type:
+  * There are several different job managers and different ways of setting up HPC computer systems. In practice I prefer not to assume that a job that is submitted to a different server will know how to find the different commands or even files. So I like to include the full paths for both. In order to find where the ''blastx'' command is located I simply type:
 <code>
@@ Line 26: / Line 26: @@
 </code>
-  - Edit the ''contigs.fa.nr.sbatch'' file to include all changes. Final script looks like this:
+  * Edit the ''contigs.fa.nr.sbatch'' file to include all changes. Final script looks like this:
 <code>
@@ Line 37: / Line 37: @@
 </code>
-  - Run the sbatch file. As soon as you run the file a job id will be assigned to your submission.
+  * Run the sbatch file. As soon as you run the file a job id will be assigned to your submission.
 <code>