Commit e0ea8a78 authored by Michael Krause's avatar Michael Krause 🎉
Browse files
parents e950a469 2ca1ebda
Pipeline #8387 passed with stages
in 38 seconds
......@@ -28,7 +28,7 @@ Wrap bash commands into a job on the fly:
.. code-block:: bash
sbatch --wrap "module load R ; Rscript main.R"
sbatch --wrap ". /etc/profile ; module load R ; Rscript main.R"
......@@ -47,7 +47,7 @@ for all combinations of subjects and runs in parallel all in one go:
sed -i "s|%RUN%|$run|g" $featfile
# submit the feat command with the current design file
sbatch --wrap "module load fsl ; feat $featfile"
sbatch --wrap ". /etc/profile ; module load fsl ; feat $featfile"
......@@ -57,7 +57,7 @@ In a job context you would just run :program:`matlab -r main` with main.m contai
.. code-block:: bash
sbatch --wrap "module load matlab/R2014b; matlab -r main"
sbatch --wrap ". /etc/profile ; module load matlab/R2014b; matlab -r main"
......@@ -202,7 +202,7 @@ template:
for image in tp2/Old/*.nii ; do
sed "s#%%IMAGE%%#$fullpath#" batch.template > batch_${i}.m
sbatch --wrap "module load spm12 ; /mcr batch $PWD/batch_${i}.m"
sbatch --wrap ". /etc/profile ; module load spm12 ; /mcr batch $PWD/batch_${i}.m"
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