Merge branch 'master' of https://git.mpib-berlin.mpg.de/krause/tardis-doc

rm/slurm/commands.rst

@@ -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"
 
 **Interactively/Blocking**
 

software/fsl.rst

@@ -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"
         done
       done
 

software/matlab.rst

@@ -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
        fullpath=$PWD/$image
        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))
    done