I have the following shell script.
#!/bin/bash --login
#BSUB -q q_ab_mpc_work
#BSUB -J psipred
#BSUB -W 01:00
#BSUB -n 64
#BSUB -o psipred.out
#BSUB -e psipred.err
module load compiler/gnu-4.8.0
module load R/3.0.1
export OMP_NUM_THREADS=4
code=${HOME}/Phd/script_dev/rfpipeline.sh
MYPATH=$HOME/Phd/script_dev/
cd ${MYPATH}
${code} myfile.txt
in which I can use bsub to submit program to cluster:
bsub < myprogram.sh
however I change the last line in my program to:
${code} $1
where I use a command line argument to specify the file, how can I pass this to bsub?
I have tried:
bsub < myprogram.sh myfile.text
however bsub will not accept myfile.text as a bash parameter.
I have also tried
bsub <<< myprogram.sh myfile.text
./myprogram.sh myfile.text | bsub
bsub "sh ./myprogram.sh myfile.text"
what do I need to do?
2 Answers
Can I answer my own question?
It seems that I can use sed to modify the file on the fly. My original file is now:
#!/bin/bash --login
#BSUB -q q_ab_mpc_work
#BSUB -J psipred
#BSUB -W 01:00
#BSUB -n 64
#BSUB -o psipred.out
#BSUB -e psipred.err
module load compiler/gnu-4.8.0
module load R/3.0.1
export OMP_NUM_THREADS=4
code=${HOME}/Phd/script_dev/rfpipeline.sh
MYPATH=$HOME/Phd/script_dev/
cd ${MYPATH}
${code} myfile
and I wrote a bash script, sender.sh to both modify the variable myfile with a command line argument, and send the modified file off to bsub:
#!/bin/bash
sed "s/myfile/$1/g" < myprogram.sh | bsub
being careful to use double quotes so that bash does not read $ literally. I then simply run ./sender.sh jobfile.txt which works!
Hope this helps anybody.
This answer should resolve your problem:
Just pass the script with arguments at the end of the bsub command.
Ex. example.sh
#!/bin/bash
export input=${1}
echo "arg input: ${input}"
bsub command:
bsub [bsub args] "path/to/example.sh arg1"
