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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 07:58] – [Some more useful SLURM notes] 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 ===
+<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>