Commit efa02ee8 authored by Michael Krause's avatar Michael Krause 🎉
Browse files

Fix bash syntax highlighting

parent 3dcc9863
...@@ -36,16 +36,16 @@ for all combinations of subjects and runs in parallel all in one go: ...@@ -36,16 +36,16 @@ for all combinations of subjects and runs in parallel all in one go:
.. code-block:: bash .. code-block:: bash
for subject in ID1 ID2 ID3; do for subject in ID1 ID2 ID3; do
for run in 1 2 3 ; do for run in 1 2 3 ; do
# create a copy of the template with a unique name # create a copy of the template with a unique name
featfile="design.${subject}.${run}.fsf" featfile="design.${subject}.${run}.fsf"
cp design.template $featfile cp design.template $featfile
# replace the placeholder by actual values # replace the placeholder by actual values
sed -i "s|%SUBJECT%|$subject|g" $featfile sed -i "s|%SUBJECT%|$subject|g" $featfile
sed -i "s|%RUN%|$run|g" $featfile sed -i "s|%RUN%|$run|g" $featfile
# submit the feat command with the current design file # submit the feat command with the current design file
sbatch --wrap ". /etc/profile ; module load fsl ; feat $featfile" sbatch --wrap ". /etc/profile ; module load fsl ; feat $featfile"
done done
...@@ -62,7 +62,7 @@ parallelize over a number of subjects. Example: ...@@ -62,7 +62,7 @@ parallelize over a number of subjects. Example:
.. code-block:: bash .. code-block:: bash
for icadir in *ica ; do for icadir in *ica ; do
echo '#!/bin/bash" > tmp.sh echo "#!/bin/bash" > tmp.sh
echo "module load fsl_fix" >> tmp.sh echo "module load fsl_fix" >> tmp.sh
echo "source /etc/fsl/5.0/fsl.sh" >> tmp.sh echo "source /etc/fsl/5.0/fsl.sh" >> tmp.sh
echo "fix ${icadir} /opt/software/fix/1.06/training_files/Standard.RData 20" >> tmp.sh echo "fix ${icadir} /opt/software/fix/1.06/training_files/Standard.RData 20" >> tmp.sh
......
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