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[WIP] Implement easier singularity compatibility #166

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feat(sing compat): Implement bash scripts to switch between docker an…
…d singularity
dnwissel committed Jan 18, 2023
commit 9a274c09958a53c80269d4fed7a8cf9b68f67455
5 changes: 5 additions & 0 deletions setup_docker.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
sed -i.bak 's/.\/singularity_images\/pwiz_sandbox/chambm\/pwiz-skyline-i-agree-to-the-vendor-licenses/g' \
nextflow.config &&
rm nextflow.config.bak
sed -i.bak 's/singularity.enabled/docker.enabled/g' nextflow.config &&
rm nextflow.config.bak
6 changes: 6 additions & 0 deletions setup_singularity.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
bash download_pwiz_sandbox.sh
sed -i.bak 's/chambm\/pwiz-skyline-i-agree-to-the-vendor-licenses/.\/singularity_images\/pwiz_sandbox/g' \
nextflow.config &&
rm nextflow.config.bak
sed -i.bak 's/docker.enabled/singularity.enabled/g' nextflow.config &&
rm nextflow.config.bak