How to do parallel search of smi files on the cluster: Difference between revisions
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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"