Created
October 18, 2012 15:08
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Submit script for calculating robustness
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#!/bin/sh | |
pdb_dir=$1 | |
# test the input to be correct | |
if [ "x" = "x$pdb_dir" ]; then | |
echo "Please specify a pdb directory" | |
exit 1 | |
fi | |
# Make the condor output directory | |
mkdir -p condor_out | |
# First, create base submit file | |
cat > submit.condor << EOF | |
universe = vanilla | |
arguments = \$(PDB_FILE_BASENAME) \$(PROCESS) | |
should_transfer_files = YES | |
when_to_transfer_output = ON_EXIT | |
output = condor_out/output.\$(PDB_FILE_BASENAME).\$(PROCESS) | |
error = condor_out/error.\$(PDB_FILE_BASENAME).\$(PROCESS) | |
executable = wrapper.sh | |
transfer_input_files = scwrl4_lin, \$(PDB_FILE), calculaterobustnessLOOP, dnaseqs | |
log = condor.log | |
EOF | |
# Count the number of lines in aastable and divide by 10 | |
lines=`wc -l dnaseqs | awk '{print $1}'` | |
num_submits=$(($lines / 10)) | |
# Now, for each pdb file in the directory given as the argument, create a submit line | |
for pdb_file in `find $pdb_dir -type f`; do | |
cat >> submit.condor << EOF | |
PDB_FILE=$pdb_file | |
PDB_FILE_BASENAME=`basename $pdb_file` | |
queue $num_submits | |
EOF | |
done | |
# Print a helpful message | |
echo "Created a condor submit file submit.condor" | |
echo "To submit the job, issue the command:" | |
echo "condor_submit submit.condor" |
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# $1 = pdb file | |
# $2 = run number | |
pdb_file=$1 | |
run_number=$2 | |
# First, make the dnaseqs file | |
linesperrun=10 | |
# Find what line number to start at | |
start_line=$((linesperrun*run_number)) | |
echo "Before" | |
ls -l | |
cat dnaseqs | head -n $start_line | tail -n $linesperrun > dnaseqs.new | |
mv dnaseqs.new dnaseqs | |
./calculaterobustnessLOOP $pdb_file | |
rm dnaseqs |
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