Commit 21eaae1c authored by Sebastien Carrere's avatar Sebastien Carrere
Browse files

example of %apprun use

parent 0f5ab99a
# 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
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 "$@"
%appenv seqtk
export LC_ALL=C
. /usr/local/etc/profile.d/conda.sh
conda activate seqtk
%apprun seqtk
exec "$@"
name: kallisto
channels:
- conda-forge
- bioconda
dependencies:
- kallisto=0.43.0=hdf51.8.17_2
name: seqtk
channels:
- bioconda
dependencies:
- seqtk=1.2=1
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