MAKING A REGULAR TEXT FILE INTO AN EXECUTABLE SCRIPT

Make a file named blasto.txt
Type$ vim blasto.txt

Begin your file with: #!/bin/sh     
This code indicates that the file is a shell script.

Then list the set of commands that you would like to execute. If you provide the absolute location of the input files then you can run the executable script from any location. Otherwise if you use ./ABP_MAP.txt instead of /home/htran/cytoSeq/ABP_MAP.txt, then the executable script will look in the current directory. End each command with an ampersand (&) to make it run in the background and allow the server to use several different cpu's.

***************Sample text file to be converted to an executable file (in this example, file is saved as "blasto.txt"):

#!/bin/sh
blastall -p blastp -d /usr/local/blast/db/TIGR/rice/OSA1.pep -i /home/htran/cytoSeq/ABP_MAP.txt -o ABP_MAP.out -e 1e-6 -v 1000 -b 1000 &
blastall -p blastp -d /usr/local/blast/db/TIGR/rice/OSA1.pep -i /home/htran/cytoSeq/ABPmotor.txt -o ABPmotor.out -e 1e-6 -v 1000 -b 1000 &
blastall -p blastp -d /usr/local/blast/db/TIGR/rice/OSA1.pep -i /home/htran/cytoSeq/ABPnon.txt -o ABPnon.out -e 1e-6 -v 1000 -b 1000 &
blastall -p blastp -d /usr/local/blast/db/TIGR/rice/OSA1.pep -i /home/htran/cytoSeq/CSactin.txt -o CSactin.out -e 1e-6 -v 1000 -b 1000 &
blastall -p blastp -d /usr/local/blast/db/TIGR/rice/OSA1.pep -i /home/htran/cytoSeq/CStubulin.txt -o CStubulin.out -e 1e-6 -v 1000 -b 1000 &
blastall -p blastp -d /usr/local/blast/db/TIGR/rice/OSA1.pep -i /home/htran/cytoSeq/MAPmotor.txt -o MAPmotor.out -e 1e-6 -v 1000 -b 1000 &
blastall -p blastp -d /usr/local/blast/db/TIGR/rice/OSA1.pep -i /home/htran/cytoSeq/MAPnon.txt -o MAPnon.out -e 1e-6 -v 1000 -b 1000 &

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Press esc
Type$ :wq 
To write and quit, saving the text file in the current directory.

Type$ chmod +x blasto.txt
This changes the permissions to execute in all three triplets.
	rwx -> read write execute
	first triplet -> user (u)
	second triplet -> group (g)
	third triplet -> other or world (o)

Type$ ll 
This checks if x is added to all three permissions.

Type$ ./blasto.txt
This executes the commands saved in blasto.txt, ./ tells the computer to look in the current directory.

Type$ ps
or
Type$ top
To check if all jobs are running.