Merge pull request #10 from frheault/release_instruction

Add informations about containers

README.md

@@ -3,7 +3,7 @@
 
 Run the RecobundlesX pipeline.
 To access the example atlases:
-https://zenodo.org/record/4104300#.X4xdG51KhdU
+https://zenodo.org/record/4630660#.YJvmwXVKhdU
 
 If you use this pipeline, please cite:
 
@@ -30,6 +30,19 @@ Requirements
 - [scilpy](https://github.com/scilus/scilpy)
 - [ants](https://github.com/ANTsX/ANTs)
 
+Singularity/Docker
+-----------
+If you are on Linux, we recommend using the Singularity to run rbx_flow pipeline.
+If you have Singularity == 3.*, launch your Nextflow command with:
+`-with-singularity scilus/scilus:1.1.0_rbxflow-1.0.0`
+
+If you have rebuild singularity Singularity == 2.* image is available [here](http://scil.dinf.usherbrooke.ca/en/containers_list/scilus-1.1.0_rbxflow-1.0.0.img)
+Launch your Nextflow command with: `-with-singularity ABSOLUTE_PATH/scilus-1.1.0_rbxflow-1.0.0.img`
+
+If you are on MacOS or Windows, we recommend using the Docker container to run rbx_flow pipeline.
+Launch your Nextflow command with:
+`-with-docker scilus/scilus:1.1.0_rbxflow-1.0.0`
+
 Usage
 -----
 

USAGE

@@ -4,6 +4,11 @@ Pipeline for RecobundlesX tractography
 USAGE
 
 nextflow run main.nf --input ... [OPTIONAL_ARGUMENTS]
+To call with a container add:
+    -with-singularity scilus/scilus:1.1.0_rbxflow-1.0.0
+    -with-docker scilus/scilus:1.1.0_rbxflow-1.0.0
+
+The recommanded atlas is available at https://zenodo.org/record/4630660#.YJvmwXVKhdU
 
 DESCRIPTION
 
@@ -22,7 +27,7 @@ DESCRIPTION
 
     OPTIONAL ARGUMENTS (current value)
 
-    --atlas_centroids                       Folder containing centroids (trk) for future tractometry (Must have the same filename as in the atlas_config)
+    --atlas_centroids                       Folder containing centroids (trk) for future tractometry (Must have the same basename as in the atlas_config + '_centroids')
 
     --multi_parameters                      Number of executions for the multi-parameters ($multi_parameters)
     --minimal_vote_ratio                    Percentage of the vote to obtain in order to be considered valid ($minimal_vote_ratio)