Simplified render script

jenfransson · Feb 5, 2024 · 60a6a75 · 60a6a75
1 parent a8c09b4
commit 60a6a75
Showing 1 changed file with 25 additions and 23 deletions.
diff --git a/scripts/render.sh b/scripts/render.sh
@@ -32,42 +32,44 @@ fi
 # start time for whole script
 start=$(date +%s.%N)
 
+# -u 1000:1000 is useful on linux
+
 ## seurat
 echo "Rendering Seurat files..."
 start_seurat=$(date +%s.%N)
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_01_qc.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_02_dimred.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_03_integration.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_04_clustering.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_05_dge.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_06_celltyping.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_07_trajectory.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_seurat_spatial quarto render /work/labs/seurat/seurat_08_spatial.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_01_qc.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_02_dimred.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_03_integration.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_04_clustering.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_05_dge.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_06_celltyping.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_seurat quarto render /work/labs/seurat/seurat_07_trajectory.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_seurat_spatial quarto render /work/labs/seurat/seurat_08_spatial.qmd
 duration_seurat=$(echo "$(date +%s.%N) - $start_seurat" | bc) && echo "Seurat time elapsed: $duration_seurat seconds"
 
 ## bioconductor
 echo "Rendering Bioconductor files..."
 start_bioc=$(date +%s.%N)
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_01_qc.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_02_dimred.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_03_integration.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_04_clustering.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_05_dge.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_06_celltyping.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/work $docker_bioc_spatial quarto render /work/labs/bioc/bioc_08_spatial.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_01_qc.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_02_dimred.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_03_integration.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_04_clustering.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_05_dge.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_bioc quarto render /work/labs/bioc/bioc_06_celltyping.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_bioc_spatial quarto render /work/labs/bioc/bioc_08_spatial.qmd
 duration_bioc=$(echo "$(date +%s.%N) - $start_bioc" | bc) && echo "Bioc time elapsed: $duration_bioc seconds"
 
 ## scanpy
 echo "Rendering Scanpy files..."
 start_scanpy=$(date +%s.%N)
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8888:8888 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_01_qc.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8888:8888 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_02_dimred.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8888:8888 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_03_integration.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8888:8888 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_04_clustering.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8888:8888 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_05_dge.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8888:8888 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_06_celltyping.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8888:8888 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_07_trajectory.qmd
-docker run --rm --platform=linux/amd64 -u 1000:1000 -p 8888:8888 -v ${PWD}:/work $docker_scanpy_spatial quarto render /work/labs/scanpy/scanpy_08_spatial.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_01_qc.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_02_dimred.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_03_integration.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_04_clustering.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_05_dge.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_06_celltyping.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_scanpy quarto render /work/labs/scanpy/scanpy_07_trajectory.qmd
+docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work $docker_scanpy_spatial quarto render /work/labs/scanpy/scanpy_08_spatial.qmd
 duration_scanpy=$(echo "$(date +%s.%N) - $start_scanpy" | bc) && echo "Scanpy time elapsed: $duration_scanpy seconds"
 
 ## site