Merge pull request #263 from LCSB-BioCore/lh-add-singularity

add singularity container Former-commit-id: 8bad816
LCSB-BioCore · Jun 2, 2021 · 4d009b6 · 4d009b6
2 parents f79da27 + c48aa38
commit 4d009b6
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diff --git a/.gitignore b/.gitignore
@@ -40,3 +40,6 @@ docs/src/notebooks/
 docs/src/index.md
 docs/src/howToContribute.md
 docs/src/assets/output.gif
+
+# ignore container files
+*.sif
diff --git a/cobrexa.def b/cobrexa.def
@@ -0,0 +1,22 @@
+Bootstrap: library
+From: crown421/default/juliabase:latest
+
+%setup
+    dir=`pwd`
+    git clone \
+    "file://$dir" \
+    ${SINGULARITY_ROOTFS}/project
+
+%post
+    export JULIA_DEPOT_PATH=/user/.julia
+    export PATH=/opt/julia/bin:$PATH
+
+    cd project
+    julia --project -e 'import Pkg; Pkg.instantiate(); Pkg.build(); Pkg.precompile();'
+
+    echo 'using COBREXA; COBREXA._print_banner();' > /project/.startup.jl
+
+    chmod -R a+rX $JULIA_DEPOT_PATH
+
+%runscript
+  julia --banner=no --project=/project --compile=min -i /project/.startup.jl