example of %apprun use

Singularity/05.singularity-app/README.md

+# BUILD AVEC PLUSIEURS ENVIRONNEMENTS CONDA ACTIVES A LA DEMANDE
+
+- base miniconda
+- install de packages de base via apt
+- install des outils avec differents environnements conda (incompatibilités de dépendances)
+- utilisation des %app* pour activer à la demande les envionnements 
+
+# COMMAND
+
+## BUILD
+
+	singularity build --fakeroot singularity-app.sif Singularity
+
+## HELP
+
+	singularity run-help singularity-app.sif
+
+## TEST
+	singularity test singularity-app.sif
+
+## USE
+
+	singularity run --app kallisto singularity-app.sif kallisto version
+	singularity run --app seqtk singularity-app.sif seqtk
+ 

Singularity/05.singularity-app/Singularity

+Bootstrap: docker
+From: conda/miniconda3
+IncludeCmd: yes
+
+%files
+
+tools/kallisto.yml /kallisto.yml
+tools/seqtk.yml /seqtk.yml
+
+%help
+Contains :
+	- kallisto 
+	- RSeqQC
+
+%labels
+    Maintainer Sebastien.Carrere@inrae.fr
+    Version v1.0
+    
+%post
+
+apt-get update && apt-get install -y  procps 
+conda update --all 
+conda env create -n kallisto -f /kallisto.yml
+conda env create -n seqtk -f /seqtk.yml
+conda clean -a
+apt clean
+
+%test
+. /usr/local/etc/profile.d/conda.sh
+echo "[Test] kallisto version"
+conda activate kallisto && kallisto version
+echo "[Test] seqtk"
+conda activate seqtk && seqtk  2>&1  | grep Version 
+
+%appenv kallisto
+export LC_ALL=C
+. /usr/local/etc/profile.d/conda.sh
+conda activate kallisto
+
+%apprun kallisto
+exec "$@"
+
+%appenv seqtk
+export LC_ALL=C
+. /usr/local/etc/profile.d/conda.sh
+conda activate seqtk
+
+%apprun seqtk
+exec "$@"
+
+

Singularity/05.singularity-app/tools/kallisto.yml

+name: kallisto
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+   - kallisto=0.43.0=hdf51.8.17_2

Singularity/05.singularity-app/tools/seqtk.yml

+name: seqtk
+channels:
+  - bioconda
+dependencies:
+  - seqtk=1.2=1