Enable vizapp

astrocyte_pkg.yml

@@ -160,3 +160,21 @@ workflow_parameters:
       metadata file that lists the batch variable (i.e, "sample"). If only
       one sample is present or batch correction is not desired, leave this
       field blank.
+
+# -----------------------------------------------------------------------------
+# SHINY APP CONFIGURATION
+# -----------------------------------------------------------------------------
+
+# Remember - The vizapp is always 'vizapp/server.R' 'vizapp/ui.R'
+#            The workflow must publish all final output into $baseDir
+
+# List of any full path of the containers
+vizapp_containers:
+  - docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/strand-lab/cellxgene/cellxgene_vip:3.1-small
+
+# List of any path of the scripts in 'your_astrocyte_workflow/vizapp' folder to run the containers
+vizapp_container_runscripts:
+  - run_container.sh
+
+# Partition to use for Vizapp jobs
+vizapp_slurm_partition: 256GB,512GB

vizapp/run_container.sh

+#!/bin/bash
+
+# Modified from https://git.biohpc.swmed.edu/CRI/scVizIt/-/blob/f18970aa0354c41f616b5308b9a7279ba79d7496/vizapp/run_container.sh
+
+# Get the parent path of this script
+SOURCE=${BASH_SOURCE[0]}
+while [ -L "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
+  SOURCE=$(readlink "$SOURCE")
+  [[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
+
+
+# Image settings
+REPO="cellxgene_vip"
+TAG="3.1-small"
+singularity_image=${REPO}-${TAG}.img
+
+outputDir=${outputDir:-"${DIR}/../workflow/output/CELLxGENE/"}
+
+# Run container
+module load singularity/3.9.9
+SINGULARITYENV_outputDir=$outputDir \
+
+### TESTING ###
+# If input is larger than 10GB, load in backed mode
+# This will reduce time to start and should help with DEA
+# But may break some other things
+#if [ $(stat -c %s ${outputDir}/cxg_input.h5ad) -gt 10000000000 ]; then
+#  backed='--backed'
+#fi
+
+# Load user-submitted annotations if present
+# Removed in favor of VIP functions
+#if [[ -f ${outputDir}/gene_set.csv ]]; then
+#  singularity exec ${singularity_image} \
+#  cellxgene launch \
+#  --host 0.0.0.0 \
+#  --port 8123 \
+#  --gene-sets-file ${outputDir}/gene_set.csv \
+#  ${outputDir}/cxg_input.h5ad
+
+# Otherwise initialize annotation output
+singularity exec ${singularity_image} \
+cellxgene launch \
+--host 0.0.0.0 \
+--port 8123 \
+--annotations-dir ${outputDir} \
+${outputDir}/cxg_input.h5ad