Merge branch 'master' of github.com:ReproNim/containers

* 'master' of github.com:ReproNim/containers:
  fix shellcheck
  Add instructions on how to deal with license files

Author: yarikoptic

README.md

@@ -339,6 +339,19 @@ on if you need to extend or redo your analysis.
   remote resources, see [ReproNim/reproman PR#438](https://github.com/ReproNim/reproman/pull/438);
 - a copy of the dataset is made available from [`///repronim/ds000003-qc`](http://datasets.datalad.org/?dir=/repronim/ds000003-qc)
   and [https://github.com/ReproNim/ds000003-qc]().
+- if you would like to create `licenses/` folder in your project datasets
+  to e.g. contain license for freesurfer, then you better add them to git-annex.
+  Following commands provide one way to do it:
+
+```shell
+mkdir licenses
+# instruct git-annex to add license files to annex, but this added file with instructions to git
+echo -e '* annex.largefiles=anything\n.gitattributes annex.largefiles=nothing' > licenses/.gitattributes
+datalad save -m "Add licenses must go into git-annex so I could avoid sharing them" licenses/.gitattributes
+cp ~/.freesurfer-license licenses/freesurfer
+datalad save -m 'added freesurfer license' licenses/freesurfer
+```
+
 
 
 # Installation

scripts/check_images--help

@@ -3,6 +3,6 @@
 #
 # Inspired by  https://github.com/ReproNim/containers/issues/137#issuecomment-2877505303
 #
-git annex find --in here | grep '\.si*' | while read f; do
+git annex find --in here | grep '\.si*' | while read -r f; do
     { singularity run "$f" --help 2>&1 && echo "$f: ok" || echo "$f: failed to execute --help" >&2; } | grep -q "no runscript" && echo "$f: no runscript" >&2; 
 done