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--- mkatari-bioinformatics-august-2013-more-slurm [2014/06/09 07:53] – created mkatari
+++ mkatari-bioinformatics-august-2013-more-slurm [2014/06/09 08:06] – mkatari
@@ Line 20: / Line 20: @@
 INPUT=$1
-OUTPUT=$INPUT.output2
+OUTPUT=$INPUT.output
 module load blast/2.2.28+
@@ Line 32: / Line 32: @@
 </code>
+=== 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.
+<code>
+#!/bin/env bash
+#SBATCH -p batch
+#SBATCH -J blastn
+#SBATCH -n 4
+#results of the ls command is captured in the variable FILES
+FILES=`ls test*fa`
+#loop through all files in FILES and each iteration, INPUT will have name of one file
+for INPUT in $FILES
+do
+#this line gets printed into screen
+echo "file name "$INPUT
+#creating variables to store values
+SBATCH=$INPUT.blast.sbatch
+OUTPUT=$INPUT.output
+#the following echo is going to be saved in sbatch file to be executed later
+echo "#!/bin/env bash
+#SBATCH -p batch
+#SBATCH -J blastn
+#SBATCH -n 4
+module load blast/2.2.28+
+echo \"Ready to run Blast\"
+blastn -query $INPUT -db nt -out $OUTPUT -num_threads 4
+echo \"Blast Done\"
+" > $SBATCH
+#now that the file is done writing, execute the sbatch file
+sbatch $SBATCH
+#end of the loop. code will be repeated (starting at "do") until all files in FILES is done.
+done
+</code>