Commit 2ca1ebda authored by Michael Krause's avatar Michael Krause 🎉
Browse files

various: missing . /etc/profile for module cmd

parent ee7b975d
Pipeline #7284 passed with stages
in 35 seconds
...@@ -28,7 +28,7 @@ Wrap bash commands into a job on the fly: ...@@ -28,7 +28,7 @@ Wrap bash commands into a job on the fly:
.. code-block:: bash .. code-block:: bash
sbatch --wrap "module load R ; Rscript main.R" sbatch --wrap ". /etc/profile ; module load R ; Rscript main.R"
**Interactively/Blocking** **Interactively/Blocking**
......
...@@ -47,7 +47,7 @@ for all combinations of subjects and runs in parallel all in one go: ...@@ -47,7 +47,7 @@ for all combinations of subjects and runs in parallel all in one go:
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 "module load fsl ; feat $featfile" sbatch --wrap ". /etc/profile ; module load fsl ; feat $featfile"
done done
done done
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...@@ -57,7 +57,7 @@ In a job context you would just run :program:`matlab -r main` with main.m contai ...@@ -57,7 +57,7 @@ In a job context you would just run :program:`matlab -r main` with main.m contai
.. code-block:: bash .. code-block:: bash
sbatch --wrap "module load matlab/R2014b; matlab -r main" sbatch --wrap ". /etc/profile ; module load matlab/R2014b; matlab -r main"
...@@ -202,7 +202,7 @@ template: ...@@ -202,7 +202,7 @@ template:
for image in tp2/Old/*.nii ; do for image in tp2/Old/*.nii ; do
fullpath=$PWD/$image fullpath=$PWD/$image
sed "s#%%IMAGE%%#$fullpath#" batch.template > batch_${i}.m sed "s#%%IMAGE%%#$fullpath#" batch.template > batch_${i}.m
sbatch --wrap "module load spm12 ; run_spm12.sh /mcr batch $PWD/batch_${i}.m" sbatch --wrap ". /etc/profile ; module load spm12 ; run_spm12.sh /mcr batch $PWD/batch_${i}.m"
i=$((i+1)) i=$((i+1))
done done
......
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