## This script contains all commands executed in the PROJECT icmuj3 and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT icmuj3 / ASAP49**********************'
echo '***************************************************************************************'

## CONFIGURATION (edit below to match your machine; lines until the separator)
export ASAP_PROJECTS_DIR=/asap_projects ## change this to write analysis results there (there will be subdirectory for each project key).
export LOOM_DIR=$ASAP_PROJECTS_DIR/loom_files
export ASAP_DATA_DB_HOST=localhost; export ASAP_DATA_DB_PORT=5432
export PSQL_DIR=/usr/pgsql-10/bin

## =========================================================

export PROJECT_DIR=$ASAP_PROJECTS_DIR/icmuj3
## Pull Docker images (must run before any docker run in this script)

docker pull fabdavid/asap_run:v5

## Host LOOM staging directory (inside Docker volume)
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $LOOM_DIR; chmod 777 $LOOM_DIR"

echo 'This project is PUBLIC => Nothing to do'

## Local PostgreSQL: create ASAP data database and load dump if missing
if ! psql -lqt | cut -d \| -f 1 | grep -qw asap_data_v5; then echo 'Create database asap_data_v5'; echo '$PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v5'; $PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v5; echo 'wget -qO - https://asap.epfl.ch/dumps/asap_data_v5.sql.gz | gunzip | grep -v \'AS integer\' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v5'; wget -qO - https://asap.epfl.ch/dumps/asap_data_v5.sql.gz | gunzip | grep -v 'AS integer' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v5; fi

## Project directory on the shared volume
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR"

## Step output directories (one folder per pipeline step that has runs)
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/parsing/ && mkdir -p $PROJECT_DIR/normalization/ && mkdir -p $PROJECT_DIR/markers/ && mkdir -p $PROJECT_DIR/marker_enrich/"

## Parsed LOOM file (public: wget; private: place file then symlink as below)
echo 'Loading parsed Loom file...'
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "wget -qO $PROJECT_DIR/parsing/output.loom 'https://asap.epfl.ch/projects/icmuj3/get_file?filename=parsing/output.loom'"

## Re-execute each recorded run (parsing step is skipped; LOOM is already in place)


## ----------------------------------------------------------------
## Run 73645  Normalization  (Normalization #1 asap_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/normalization/73645/"

## Running Normalization [73645] [Normalization #1 asap_seurat] (input_matrix:parsing)
echo '-> Running Normalization [73645] [Normalization #1 asap_seurat] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_73645 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Normalization -loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/normalization/73645/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/icmuj3/normalization/73645/exec.out 2> /data/asap2/users/1/icmuj3/normalization/73645/exec.err'"


## ----------------------------------------------------------------
## Run 159620  Find markers  (Find markers #1 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/159620/"

## Running Find markers [159620] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [159620] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_159620 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/159620 --iAnnot /col_attrs/annotation --id 469002  1> /data/asap2/users/1/icmuj3/markers/159620/exec.out 2> /data/asap2/users/1/icmuj3/markers/159620/exec.err'"


## ----------------------------------------------------------------
## Run 159621  Marker enrichment  (Marker enrichment #2 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/159621/"

## Running Marker enrichment [159621] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [159621] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_159621 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/159620 -o /data/asap2/users/1/icmuj3/markers/159621 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/159621/exec.out 2> /data/asap2/users/1/icmuj3/markers/159621/exec.err'"


## ----------------------------------------------------------------
## Run 249832  Find markers  (Find markers #2 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/249832/"

## Running Find markers [249832] [Find markers #2 asap_markers] ()
echo '-> Running Find markers [249832] [Find markers #2 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_249832 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/249832 --iAnnot /col_attrs/annotation_broad --id 468965 --is_count_table  1> /data/asap2/users/1/icmuj3/markers/249832/exec.out 2> /data/asap2/users/1/icmuj3/markers/249832/exec.err'"


## ----------------------------------------------------------------
## Run 249833  Marker enrichment  (Marker enrichment #3 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/249833/"

## Running Marker enrichment [249833] [Marker enrichment #3 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [249833] [Marker enrichment #3 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_249833 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/249832 -o /data/asap2/users/1/icmuj3/markers/249833 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/249833/exec.out 2> /data/asap2/users/1/icmuj3/markers/249833/exec.err'"


## ----------------------------------------------------------------
## Run 296113  Find markers  (Find markers #3 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/296113/"

## Running Find markers [296113] [Find markers #3 asap_markers] ()
echo '-> Running Find markers [296113] [Find markers #3 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_296113 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/296113 --iAnnot /col_attrs/ClusterID --id 468966 --is_count_table  1> /data/asap2/users/1/icmuj3/markers/296113/exec.out 2> /data/asap2/users/1/icmuj3/markers/296113/exec.err'"


## ----------------------------------------------------------------
## Run 296114  Marker enrichment  (Marker enrichment #4 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/296114/"

## Running Marker enrichment [296114] [Marker enrichment #4 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [296114] [Marker enrichment #4 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_296114 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/296113 -o /data/asap2/users/1/icmuj3/markers/296114 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/296114/exec.out 2> /data/asap2/users/1/icmuj3/markers/296114/exec.err'"


## ----------------------------------------------------------------
## Run 300650  Find markers  (Find markers #4 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/300650/"

## Running Find markers [300650] [Find markers #4 asap_markers] ()
echo '-> Running Find markers [300650] [Find markers #4 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_300650 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/300650 --iAnnot /col_attrs/Clustering_Annotation --id 468991 --is_count_table  1> /data/asap2/users/1/icmuj3/markers/300650/exec.out 2> /data/asap2/users/1/icmuj3/markers/300650/exec.err'"


## ----------------------------------------------------------------
## Run 300651  Marker enrichment  (Marker enrichment #5 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/300651/"

## Running Marker enrichment [300651] [Marker enrichment #5 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [300651] [Marker enrichment #5 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_300651 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/300650 -o /data/asap2/users/1/icmuj3/markers/300651 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/300651/exec.out 2> /data/asap2/users/1/icmuj3/markers/300651/exec.err'"


## ----------------------------------------------------------------
## Run 300654  Find markers  (Find markers #5 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/300654/"

## Running Find markers [300654] [Find markers #5 asap_markers] ()
echo '-> Running Find markers [300654] [Find markers #5 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_300654 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/300654 --iAnnot /col_attrs/Clustering_Annotation__Relaxed_ --id 468963 --is_count_table  1> /data/asap2/users/1/icmuj3/markers/300654/exec.out 2> /data/asap2/users/1/icmuj3/markers/300654/exec.err'"


## ----------------------------------------------------------------
## Run 300655  Marker enrichment  (Marker enrichment #6 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/300655/"

## Running Marker enrichment [300655] [Marker enrichment #6 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [300655] [Marker enrichment #6 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_300655 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/300654 -o /data/asap2/users/1/icmuj3/markers/300655 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/300655/exec.out 2> /data/asap2/users/1/icmuj3/markers/300655/exec.err'"


## ----------------------------------------------------------------
## Run 300656  Find markers  (Find markers #6 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/300656/"

## Running Find markers [300656] [Find markers #6 asap_markers] ()
echo '-> Running Find markers [300656] [Find markers #6 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_300656 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/300656 --iAnnot /col_attrs/R_annotation --id 469024 --is_count_table  1> /data/asap2/users/1/icmuj3/markers/300656/exec.out 2> /data/asap2/users/1/icmuj3/markers/300656/exec.err'"


## ----------------------------------------------------------------
## Run 300657  Marker enrichment  (Marker enrichment #7 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/300657/"

## Running Marker enrichment [300657] [Marker enrichment #7 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [300657] [Marker enrichment #7 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_300657 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/300656 -o /data/asap2/users/1/icmuj3/markers/300657 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/300657/exec.out 2> /data/asap2/users/1/icmuj3/markers/300657/exec.err'"


## ----------------------------------------------------------------
## Run 306835  Find markers  (Find markers #7 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/306835/"

## Running Find markers [306835] [Find markers #7 asap_markers] ()
echo '-> Running Find markers [306835] [Find markers #7 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_306835 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/306835 --iAnnot /col_attrs/fly_genetics --id 468980 --is_count_table  1> /data/asap2/users/1/icmuj3/markers/306835/exec.out 2> /data/asap2/users/1/icmuj3/markers/306835/exec.err'"


## ----------------------------------------------------------------
## Run 306836  Marker enrichment  (Marker enrichment #8 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/306836/"

## Running Marker enrichment [306836] [Marker enrichment #8 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [306836] [Marker enrichment #8 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_306836 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/306835 -o /data/asap2/users/1/icmuj3/markers/306836 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/306836/exec.out 2> /data/asap2/users/1/icmuj3/markers/306836/exec.err'"


## ----------------------------------------------------------------
## Run 312627  Find markers  (Find markers #8 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/312627/"

## Running Find markers [312627] [Find markers #8 asap_markers] ()
echo '-> Running Find markers [312627] [Find markers #8 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_312627 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/312627 --iAnnot /col_attrs/R_annotation__ontology_id --id 469009 --is_count_table  1> /data/asap2/users/1/icmuj3/markers/312627/exec.out 2> /data/asap2/users/1/icmuj3/markers/312627/exec.err'"


## ----------------------------------------------------------------
## Run 312628  Marker enrichment  (Marker enrichment #9 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/312628/"

## Running Marker enrichment [312628] [Marker enrichment #9 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [312628] [Marker enrichment #9 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_312628 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/312627 -o /data/asap2/users/1/icmuj3/markers/312628 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/312628/exec.out 2> /data/asap2/users/1/icmuj3/markers/312628/exec.err'"


## ----------------------------------------------------------------
## Run 321447  Find markers  (Find markers #9 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/321447/"

## Running Find markers [321447] [Find markers #9 asap_markers] ()
echo '-> Running Find markers [321447] [Find markers #9 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_321447 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/321447 --iAnnot /col_attrs/Clustering_Leiden_resolution_12.0 --id 469025 --is_count_table  1> /data/asap2/users/1/icmuj3/markers/321447/exec.out 2> /data/asap2/users/1/icmuj3/markers/321447/exec.err'"


## ----------------------------------------------------------------
## Run 321448  Marker enrichment  (Marker enrichment #10 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/321448/"

## Running Marker enrichment [321448] [Marker enrichment #10 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [321448] [Marker enrichment #10 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_321448 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/321447 -o /data/asap2/users/1/icmuj3/markers/321448 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/321448/exec.out 2> /data/asap2/users/1/icmuj3/markers/321448/exec.err'"


## ----------------------------------------------------------------
## Run 342700  Find markers  (Find markers #10 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/342700/"

## Running Find markers [342700] [Find markers #10 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [342700] [Find markers #10 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_342700 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/342700 --iAnnot /col_attrs/annotation --id 469002 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/342700/exec.out 2> /data/asap2/users/1/icmuj3/markers/342700/exec.err'"


## ----------------------------------------------------------------
## Run 342701  Marker enrichment  (Marker enrichment #11 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/342701/"

## Running Marker enrichment [342701] [Marker enrichment #11 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [342701] [Marker enrichment #11 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_342701 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/342700 -o /data/asap2/users/1/icmuj3/markers/342701 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/342701/exec.out 2> /data/asap2/users/1/icmuj3/markers/342701/exec.err'"


## ----------------------------------------------------------------
## Run 348014  Find markers  (Find markers #11 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/348014/"

## Running Find markers [348014] [Find markers #11 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [348014] [Find markers #11 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_348014 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/348014 --iAnnot /col_attrs/annotation_broad --id 468965 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/348014/exec.out 2> /data/asap2/users/1/icmuj3/markers/348014/exec.err'"


## ----------------------------------------------------------------
## Run 348015  Marker enrichment  (Marker enrichment #12 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/348015/"

## Running Marker enrichment [348015] [Marker enrichment #12 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [348015] [Marker enrichment #12 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_348015 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/348014 -o /data/asap2/users/1/icmuj3/markers/348015 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/348015/exec.out 2> /data/asap2/users/1/icmuj3/markers/348015/exec.err'"


## ----------------------------------------------------------------
## Run 350663  Find markers  (Find markers #12 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/350663/"

## Running Find markers [350663] [Find markers #12 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [350663] [Find markers #12 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_350663 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/350663 --iAnnot /col_attrs/Clustering_Broad_Annotation__Relaxed_ --id 469015 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/350663/exec.out 2> /data/asap2/users/1/icmuj3/markers/350663/exec.err'"


## ----------------------------------------------------------------
## Run 350664  Marker enrichment  (Marker enrichment #13 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/350664/"

## Running Marker enrichment [350664] [Marker enrichment #13 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [350664] [Marker enrichment #13 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_350664 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/350663 -o /data/asap2/users/1/icmuj3/markers/350664 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/350664/exec.out 2> /data/asap2/users/1/icmuj3/markers/350664/exec.err'"


## ----------------------------------------------------------------
## Run 366572  Find markers  (Find markers #13 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/366572/"

## Running Find markers [366572] [Find markers #13 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [366572] [Find markers #13 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_366572 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/366572 --iAnnot /col_attrs/R_annotation --id 469024 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/366572/exec.out 2> /data/asap2/users/1/icmuj3/markers/366572/exec.err'"


## ----------------------------------------------------------------
## Run 366573  Marker enrichment  (Marker enrichment #14 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/366573/"

## Running Marker enrichment [366573] [Marker enrichment #14 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [366573] [Marker enrichment #14 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_366573 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/366572 -o /data/asap2/users/1/icmuj3/markers/366573 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/366573/exec.out 2> /data/asap2/users/1/icmuj3/markers/366573/exec.err'"


## ----------------------------------------------------------------
## Run 366574  Find markers  (Find markers #14 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/366574/"

## Running Find markers [366574] [Find markers #14 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [366574] [Find markers #14 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_366574 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/366574 --iAnnot /col_attrs/annotation__ontology_id --id 468962 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/366574/exec.out 2> /data/asap2/users/1/icmuj3/markers/366574/exec.err'"


## ----------------------------------------------------------------
## Run 366575  Marker enrichment  (Marker enrichment #15 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/366575/"

## Running Marker enrichment [366575] [Marker enrichment #15 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [366575] [Marker enrichment #15 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_366575 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/366574 -o /data/asap2/users/1/icmuj3/markers/366575 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/366575/exec.out 2> /data/asap2/users/1/icmuj3/markers/366575/exec.err'"


## ----------------------------------------------------------------
## Run 366576  Find markers  (Find markers #15 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/366576/"

## Running Find markers [366576] [Find markers #15 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [366576] [Find markers #15 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_366576 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/366576 --iAnnot /col_attrs/Clustering_Annotation --id 468991 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/366576/exec.out 2> /data/asap2/users/1/icmuj3/markers/366576/exec.err'"


## ----------------------------------------------------------------
## Run 366577  Marker enrichment  (Marker enrichment #16 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/366577/"

## Running Marker enrichment [366577] [Marker enrichment #16 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [366577] [Marker enrichment #16 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_366577 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/366576 -o /data/asap2/users/1/icmuj3/markers/366577 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/366577/exec.out 2> /data/asap2/users/1/icmuj3/markers/366577/exec.err'"


## ----------------------------------------------------------------
## Run 385821  Find markers  (Find markers #16 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/385821/"

## Running Find markers [385821] [Find markers #16 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [385821] [Find markers #16 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_385821 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/385821 --iAnnot /col_attrs/tissue --id 468996 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/385821/exec.out 2> /data/asap2/users/1/icmuj3/markers/385821/exec.err'"


## ----------------------------------------------------------------
## Run 385822  Marker enrichment  (Marker enrichment #17 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/385822/"

## Running Marker enrichment [385822] [Marker enrichment #17 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [385822] [Marker enrichment #17 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_385822 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/icmuj3/markers/385821 -o /data/asap2/users/1/icmuj3/markers/385822 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/icmuj3/markers/385822/exec.out 2> /data/asap2/users/1/icmuj3/markers/385822/exec.err'"


## ----------------------------------------------------------------
## Run 445244  Find markers  (Find markers #17 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/445244/"

## Running Find markers [445244] [Find markers #17 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [445244] [Find markers #17 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_445244 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/445244 --iAnnot /col_attrs/fca_id --id 468972 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/445244/exec.out 2> /data/asap2/users/1/icmuj3/markers/445244/exec.err'"


## ----------------------------------------------------------------
## Run 531939  Find markers  (Find markers #18 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/531939/"

## Running Find markers [531939] [Find markers #18 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [531939] [Find markers #18 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_531939 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/531939 --iAnnot /col_attrs/R_annotation_broad --id 469028 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/531939/exec.out 2> /data/asap2/users/1/icmuj3/markers/531939/exec.err'"


## ----------------------------------------------------------------
## Run 547546  Find markers  (Find markers #19 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/547546/"

## Running Find markers [547546] [Find markers #19 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [547546] [Find markers #19 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_547546 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/547546 --iAnnot /col_attrs/sample_id --id 468964 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/547546/exec.out 2> /data/asap2/users/1/icmuj3/markers/547546/exec.err'"


## ----------------------------------------------------------------
## Run 629505  Find markers  (Find markers #20 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/629505/"

## Running Find markers [629505] [Find markers #20 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [629505] [Find markers #20 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_629505 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/629505 --iAnnot /col_attrs/Clustering_Leiden_resolution_25.0 --id 468977 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/629505/exec.out 2> /data/asap2/users/1/icmuj3/markers/629505/exec.err'"


## ----------------------------------------------------------------
## Run 642373  Find markers  (Find markers #21 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/642373/"

## Running Find markers [642373] [Find markers #21 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [642373] [Find markers #21 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_642373 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/642373 --iAnnot /col_attrs/scrublet__predicted_doublets --id 468975 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/642373/exec.out 2> /data/asap2/users/1/icmuj3/markers/642373/exec.err'"


## ----------------------------------------------------------------
## Run 651942  Find markers  (Find markers #22 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/651942/"

## Running Find markers [651942] [Find markers #22 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [651942] [Find markers #22 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_651942 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/651942 --iAnnot /col_attrs/age --id 468971 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/651942/exec.out 2> /data/asap2/users/1/icmuj3/markers/651942/exec.err'"


## ----------------------------------------------------------------
## Run 652804  Find markers  (Find markers #23 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/652804/"

## Running Find markers [652804] [Find markers #23 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [652804] [Find markers #23 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_652804 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/652804 --iAnnot /col_attrs/ClusterID --id 468966 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/652804/exec.out 2> /data/asap2/users/1/icmuj3/markers/652804/exec.err'"


## ----------------------------------------------------------------
## Run 660050  Find markers  (Find markers #24 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/660050/"

## Running Find markers [660050] [Find markers #24 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [660050] [Find markers #24 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_660050 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/660050 --iAnnot /col_attrs/sex --id 469020 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/660050/exec.out 2> /data/asap2/users/1/icmuj3/markers/660050/exec.err'"


## ----------------------------------------------------------------
## Run 767891  Find markers  (Find markers #25 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/767891/"

## Running Find markers [767891] [Find markers #25 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [767891] [Find markers #25 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_767891 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR  fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/icmuj3/parsing/output.loom -o /data/asap2/users/1/icmuj3/markers/767891 --iAnnot /col_attrs/Clustering_Annotation__Relaxed_ --id 468963 --is_count_table true  1> /data/asap2/users/1/icmuj3/markers/767891/exec.out 2> /data/asap2/users/1/icmuj3/markers/767891/exec.err'"