Merge pull request #24 from cpp-lln-lab/marcobarilari-patch-1

fixes #23 - Add how to connect from outside uclouvain network

Author: marcobarilari

doc/cpp_fmriprep.slurm

@@ -22,22 +22,22 @@
 # writtent by CPP people
 #
 # Submission command for Lemaitre3
-# 
+#
 # sbatch cpp_fmriprep.slurm <subjID> <TaskName>
-# 
+#
 # examples:
 # - 1 subject 1 task
 # sbatch cpp_fmriprep.slurm sub-01 visMotLocalizer
-# 
+#
 # - 1 subject all task
 # sbatch cpp_fmriprep.slurm sub-01 ''
-# 
+#
 # - all subjects 1 task
 # sbatch cpp_fmriprep.slurm '' visMotLocalizer
-# 
+#
 # - multiple subjects
 # sbatch cpp_fmriprep.slurm 'sub-01 sub-02' visMotLocalizer
-# 
+#
 # - multiple tasks
 # sbatch cpp_fmriprep.slurm sub-01 'visMotLocalizer audMotLocalizer'
 #

doc/cpp_mriqc.slurm

@@ -22,18 +22,18 @@
 # writtent by CPP people
 #
 # Submission command for Lemaitre3
-# 
+#
 # sbatch cpp_mriqc.slurm <subjID>
-# 
+#
 # examples:
 # - 1 subject
-# sbatch cpp_mriqc.slurm sub-01 
-# 
+# sbatch cpp_mriqc.slurm sub-01
+#
 # - all subjects
 # sbatch cpp_mriqc.slurm ''
-# 
+#
 # - multiple subjects
-# sbatch cpp_mriqc.slurm 'sub-01 sub-02' 
+# sbatch cpp_mriqc.slurm 'sub-01 sub-02'
 #
 # - submit all the subjects (1 per job) all at once
 # read subj list to submit each to a job
@@ -73,4 +73,4 @@ singularity run --cleanenv \
         "${path_to_singularity_image}" \
             /data \
             /out \
-            participant --participant-label "${subjID}" 
+            participant --participant-label "${subjID}"

doc/cpp_mriqc_group.slurm

@@ -22,7 +22,7 @@
 # writtent by CPP people
 #
 # Submission command for Lemaitre3 after running mriqc for each participant
-# 
+#
 # sbatch cpp_mriqc_group.slurm
 
 # create jobs_report folder in case they don't exist

doc/index.md

@@ -7,5 +7,16 @@ To contribute see [here](https://cpp-lln-lab.github.io/CPP_HPC/contributing/)
 This repo is a hub to centralize snippet of code, script etc to run analyses (freesurfer, fmriprep, mriqc, etc) in
 the [CECI clusters](http://www.ceci-hpc.be/) available for UCLouvain.
 
-To get an account, follow the instructions in the
+
+## FAQ
+
+It is very likely that most of the FAQ could be answered by [CECI documentation](https://support.ceci-hpc.be/doc/)
+
+### How can get a ceci account and connect to a cluster?
+
+To get an account and connect, follow the instructions in the
 [documentation](https://support.ceci-hpc.be/doc/).
+
+### How can I connect to a cluster from outside the UCLouvain network?
+
+Use a a VPN to connect as-if you are within the UCLouvain network. Check [how to use UCLouvain VPN](https://intranet.uclouvain.be/fr/myucl/services-informatiques/vpn.html)

doc/run_fmriprep.md

@@ -60,8 +60,8 @@ Content of the `cpp_fmriprep.slurm` file (download and edit from [here](cpp_fmri
 !!! Warning
 
     1. Read the fmriprep documentation to know what you are doing and how the arguments of the run call effects the results
-    2. All the paths and email are set afte Marco's users for demosntration. 
-    3. Edit the scripts with the info you need to make it run for your user from top to buttom of the script, do not over look the first "commented" chunk cause it is not a real commented section (check the email and job report path, data paths and the `username` etc.). 
+    2. All the paths and email are set afte Marco's users for demosntration.
+    3. Edit the scripts with the info you need to make it run for your user from top to buttom of the script, do not over look the first "commented" chunk cause it is not a real commented section (check the email and job report path, data paths and the `username` etc.).
 
 ```bash
 {% include "cpp_fmriprep.slurm" %}

doc/run_mriqc.md

@@ -65,8 +65,8 @@ Content of the `cpp_mriqc.slurm` file (download and edit from [here](cpp_mriqc.s
 !!! Warning
 
     1. Read the MRIqc documentation to know what you are doing and how the arguments of the run call effects the results
-    2. All the paths and email are set afte Marco's users for demosntration. 
-    3. Edit the scripts with the info you need to make it run for your user from top to buttom of the script, do not over look the first "commented" chunk cause it is not a real commented section (check the email and job report path, data paths and the `username` etc.). 
+    2. All the paths and email are set afte Marco's users for demosntration.
+    3. Edit the scripts with the info you need to make it run for your user from top to buttom of the script, do not over look the first "commented" chunk cause it is not a real commented section (check the email and job report path, data paths and the `username` etc.).
 
 ```bash
 {% include "cpp_mriqc.slurm" %}
@@ -92,15 +92,15 @@ sbatch cpp_mriqc.slurm sub-01
 ls -d sub* | xargs -n1 -I{} sbatch path/to/cpp_mriqc.slurm {}
 ```
 
-### Group level 
+### Group level
 
 Content of the `cpp_mriqc_group.slurm` file (download and edit from [here](cpp_mriqc_group.slurm))
 
 !!! Warning
 
     1. Read the MRIqc documentation to know what you are doing and how the arguments of the run call effects the results
-    2. All the paths and email are set afte Marco's users for demosntration. 
-    3. Edit the scripts with the info you need to make it run for your user from top to buttom of the script, do not over look the first "commented" chunk cause it is not a real commented section (check the email and job report path, data paths and the `username` etc.). 
+    2. All the paths and email are set afte Marco's users for demosntration.
+    3. Edit the scripts with the info you need to make it run for your user from top to buttom of the script, do not over look the first "commented" chunk cause it is not a real commented section (check the email and job report path, data paths and the `username` etc.).
 
 ```bash
 {% include "cpp_mriqc_group.slurm" %}

mkdocs.yml

@@ -14,7 +14,7 @@ theme:
     primary: light blue
     accent: light blue
   features:
-    - navigation.expand
+  - navigation.expand
 
 docs_dir: doc