Difference between revisions of "How to do parallel search of smi files on the cluster"
Jump to navigation
Jump to search
| Line 7: | Line 7: | ||
search_smi.sh | search_smi.sh | ||
merge.sh | merge.sh | ||
| + | </pre> | ||
| + | |||
| + | '''SUBMIT.sh''' | ||
| + | SUBMIT.sh contains bash code for qsub. SUBMIT.sh specify the qsub command, parameters for qsub, input file, the function script, parameters for the function. A example is shown below. | ||
| + | <pre> | ||
| + | #!/bin/bash | ||
| + | |||
| + | /nfs/soft/tools/utils/qsub-slice/qsub-mr \ | ||
| + | -l 5 \ | ||
| + | -N test \ | ||
| + | all.input \ | ||
| + | ./search_smi.sh \ | ||
| + | -q "CS(=O)(=O)CCNCc1ccccc1" | ||
</pre> | </pre> | ||
Revision as of 17:10, 19 July 2018
This tutorial shows how to do parallel search of smi files on the cluster. The files and scripts can be found in /nfs/home/jizhou/ex7/2D/test-parallel @gimel.compbio.ucsf.edu
Create a folder with the following files and scripts
SUBMIT.sh input.txt search_smi.sh merge.sh
SUBMIT.sh SUBMIT.sh contains bash code for qsub. SUBMIT.sh specify the qsub command, parameters for qsub, input file, the function script, parameters for the function. A example is shown below.
#!/bin/bash
/nfs/soft/tools/utils/qsub-slice/qsub-mr \
-l 5 \
-N test \
all.input \
./search_smi.sh \
-q "CS(=O)(=O)CCNCc1ccccc1"