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--- mkatari-bioinformatics-august-2013-more-slurm [2014/06/09 07:58] – [Some more useful SLURM notes] mkatari
+++ mkatari-bioinformatics-august-2013-more-slurm [2014/06/09 08:06] – mkatari
@@ Line 33: / Line 33: @@
 === Generating sbatch scripts on the fly ===
+In the case where you have have hundreds of files, it is still quite cumbersome to execute the same script manually. In the example below we will get a list of inputs we want to use as input and create a separate sbatch file for each of them.
+The single quote (not the apostraphe, on the US keyboard it is located to the left of 1) can be used to capture command line results. Here we get a list of fasta files that start with the word test and store it in the variable $FILES. Notice that $FILES is not just one string, but an array of files returned as a result to the ls command. Then we start a loop and work with one file at a time. At each iteration of the for loop the file name will be stored in the variable $INPUT.
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