## This script contains all commands executed in the PROJECT oqtllw and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT oqtllw / ASAP26**********************'
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/oqtllw
## 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/oqtllw/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 73691  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/73691/"

## Running Normalization [73691] [Normalization #1 asap_seurat] (input_matrix:parsing scale_factor:10000)
echo '-> Running Normalization [73691] [Normalization #1 asap_seurat] (input_matrix:parsing scale_factor:10000)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_73691 --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/oqtllw/parsing/output.loom -o /data/asap2/users/1/oqtllw/normalization/73691/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/oqtllw/normalization/73691/exec.out 2> /data/asap2/users/1/oqtllw/normalization/73691/exec.err'"


## ----------------------------------------------------------------
## Run 137516  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/137516/"

## Running Find markers [137516] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [137516] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_137516 --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/oqtllw/parsing/output.loom -o /data/asap2/users/1/oqtllw/markers/137516 --iAnnot /col_attrs/annotation --id 470547  1> /data/asap2/users/1/oqtllw/markers/137516/exec.out 2> /data/asap2/users/1/oqtllw/markers/137516/exec.err'"


## ----------------------------------------------------------------
## Run 137517  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/137517/"

## Running Marker enrichment [137517] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [137517] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_137517 --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/oqtllw/markers/137516 -o /data/asap2/users/1/oqtllw/markers/137517 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/oqtllw/markers/137517/exec.out 2> /data/asap2/users/1/oqtllw/markers/137517/exec.err'"


## ----------------------------------------------------------------
## Run 137518  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/137518/"

## Running Find markers [137518] [Find markers #2 asap_markers] ()
echo '-> Running Find markers [137518] [Find markers #2 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_137518 --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/oqtllw/parsing/output.loom -o /data/asap2/users/1/oqtllw/markers/137518 --iAnnot /col_attrs/annotation_broad --id 470517  1> /data/asap2/users/1/oqtllw/markers/137518/exec.out 2> /data/asap2/users/1/oqtllw/markers/137518/exec.err'"


## ----------------------------------------------------------------
## Run 137519  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/137519/"

## Running Marker enrichment [137519] [Marker enrichment #3 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [137519] [Marker enrichment #3 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_137519 --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/oqtllw/markers/137518 -o /data/asap2/users/1/oqtllw/markers/137519 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/oqtllw/markers/137519/exec.out 2> /data/asap2/users/1/oqtllw/markers/137519/exec.err'"


## ----------------------------------------------------------------
## Run 216868  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/216868/"

## Running Find markers [216868] [Find markers #3 asap_markers] ()
echo '-> Running Find markers [216868] [Find markers #3 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_216868 --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/oqtllw/parsing/output.loom -o /data/asap2/users/1/oqtllw/markers/216868 --iAnnot /col_attrs/S_annotation_broad --id 470524 --is_count_table   1> /data/asap2/users/1/oqtllw/markers/216868/exec.out 2> /data/asap2/users/1/oqtllw/markers/216868/exec.err'"


## ----------------------------------------------------------------
## Run 216869  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/216869/"

## Running Marker enrichment [216869] [Marker enrichment #4 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [216869] [Marker enrichment #4 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_216869 --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/oqtllw/markers/216868 -o /data/asap2/users/1/oqtllw/markers/216869 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/oqtllw/markers/216869/exec.out 2> /data/asap2/users/1/oqtllw/markers/216869/exec.err'"


## ----------------------------------------------------------------
## Run 345160  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/345160/"

## Running Find markers [345160] [Find markers #4 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [345160] [Find markers #4 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_345160 --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/oqtllw/parsing/output.loom -o /data/asap2/users/1/oqtllw/markers/345160 --iAnnot /col_attrs/annotation --id 470547 --is_count_table true  1> /data/asap2/users/1/oqtllw/markers/345160/exec.out 2> /data/asap2/users/1/oqtllw/markers/345160/exec.err'"


## ----------------------------------------------------------------
## Run 345161  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/345161/"

## Running Marker enrichment [345161] [Marker enrichment #5 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [345161] [Marker enrichment #5 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_345161 --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/oqtllw/markers/345160 -o /data/asap2/users/1/oqtllw/markers/345161 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/oqtllw/markers/345161/exec.out 2> /data/asap2/users/1/oqtllw/markers/345161/exec.err'"


## ----------------------------------------------------------------
## Run 772035  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/772035/"

## Running Find markers [772035] [Find markers #5 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772035] [Find markers #5 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772035 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772035 --iAnnot /col_attrs/annotation_broad --id 470517 --is_count_table true  1> $PROJECT_DIR/markers/772035/exec.out 2> $PROJECT_DIR/markers/772035/exec.err'"


## ----------------------------------------------------------------
## Run 772036  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/772036/"

## Running Find markers [772036] [Find markers #6 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772036] [Find markers #6 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772036 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772036 --iAnnot /col_attrs/annotation_broad --id 470517 --is_count_table true  1> $PROJECT_DIR/markers/772036/exec.out 2> $PROJECT_DIR/markers/772036/exec.err'"


## ----------------------------------------------------------------
## Run 772037  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/772037/"

## Running Find markers [772037] [Find markers #7 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772037] [Find markers #7 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772037 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772037 --iAnnot /col_attrs/annotation_broad --id 470517 --is_count_table true  1> $PROJECT_DIR/markers/772037/exec.out 2> $PROJECT_DIR/markers/772037/exec.err'"


## ----------------------------------------------------------------
## Run 772038  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/772038/"

## Running Find markers [772038] [Find markers #8 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772038] [Find markers #8 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772038 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772038 --iAnnot /col_attrs/annotation__ontology_id --id 470515 --is_count_table true  1> $PROJECT_DIR/markers/772038/exec.out 2> $PROJECT_DIR/markers/772038/exec.err'"


## ----------------------------------------------------------------
## Run 772039  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/772039/"

## Running Find markers [772039] [Find markers #9 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772039] [Find markers #9 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772039 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772039 --iAnnot /col_attrs/annotation_broad --id 470517 --is_count_table true  1> $PROJECT_DIR/markers/772039/exec.out 2> $PROJECT_DIR/markers/772039/exec.err'"


## ----------------------------------------------------------------
## Run 772040  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/772040/"

## Running Find markers [772040] [Find markers #10 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772040] [Find markers #10 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772040 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772040 --iAnnot /col_attrs/annotation --id 470547 --is_count_table true  1> $PROJECT_DIR/markers/772040/exec.out 2> $PROJECT_DIR/markers/772040/exec.err'"


## ----------------------------------------------------------------
## Run 772041  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/772041/"

## Running Find markers [772041] [Find markers #11 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772041] [Find markers #11 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772041 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772041 --iAnnot /col_attrs/batch --id 470533 --is_count_table true  1> $PROJECT_DIR/markers/772041/exec.out 2> $PROJECT_DIR/markers/772041/exec.err'"


## ----------------------------------------------------------------
## Run 772042  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/772042/"

## Running Find markers [772042] [Find markers #12 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772042] [Find markers #12 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772042 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772042 --iAnnot /col_attrs/batch_id --id 470563 --is_count_table true  1> $PROJECT_DIR/markers/772042/exec.out 2> $PROJECT_DIR/markers/772042/exec.err'"


## ----------------------------------------------------------------
## Run 772043  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/772043/"

## Running Find markers [772043] [Find markers #13 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772043] [Find markers #13 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772043 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772043 --iAnnot /col_attrs/annotation_broad__ontology_id --id 470521 --is_count_table true  1> $PROJECT_DIR/markers/772043/exec.out 2> $PROJECT_DIR/markers/772043/exec.err'"


## ----------------------------------------------------------------
## Run 772078  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/772078/"

## Running Find markers [772078] [Find markers #18 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772078] [Find markers #18 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772078 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772078 --iAnnot /col_attrs/Clustering_Leiden_resolution_0.4__default__302_ --id 470560 --is_count_table true  1> $PROJECT_DIR/markers/772078/exec.out 2> $PROJECT_DIR/markers/772078/exec.err'"


## ----------------------------------------------------------------
## Run 772079  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/772079/"

## Running Find markers [772079] [Find markers #19 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772079] [Find markers #19 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772079 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772079 --iAnnot /col_attrs/Clustering_Annotation --id 470537 --is_count_table true  1> $PROJECT_DIR/markers/772079/exec.out 2> $PROJECT_DIR/markers/772079/exec.err'"


## ----------------------------------------------------------------
## Run 772080  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/772080/"

## Running Find markers [772080] [Find markers #20 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772080] [Find markers #20 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772080 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772080 --iAnnot /col_attrs/Clustering_Annotation__Stringent_ --id 470573 --is_count_table true  1> $PROJECT_DIR/markers/772080/exec.out 2> $PROJECT_DIR/markers/772080/exec.err'"


## ----------------------------------------------------------------
## Run 772081  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/772081/"

## Running Find markers [772081] [Find markers #21 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772081] [Find markers #21 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772081 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772081 --iAnnot /col_attrs/Clustering_Broad_Annotation --id 470572 --is_count_table true  1> $PROJECT_DIR/markers/772081/exec.out 2> $PROJECT_DIR/markers/772081/exec.err'"


## ----------------------------------------------------------------
## Run 772082  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/772082/"

## Running Find markers [772082] [Find markers #22 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772082] [Find markers #22 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772082 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772082 --iAnnot /col_attrs/Clustering_Broad_Annotation_Extrapolated__Stringent_ --id 470548 --is_count_table true  1> $PROJECT_DIR/markers/772082/exec.out 2> $PROJECT_DIR/markers/772082/exec.err'"


## ----------------------------------------------------------------
## Run 772083  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/772083/"

## Running Find markers [772083] [Find markers #23 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772083] [Find markers #23 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772083 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772083 --iAnnot /col_attrs/Clustering_Broad_Annotation__Stringent_ --id 470527 --is_count_table true  1> $PROJECT_DIR/markers/772083/exec.out 2> $PROJECT_DIR/markers/772083/exec.err'"


## ----------------------------------------------------------------
## Run 772084  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/772084/"

## Running Find markers [772084] [Find markers #24 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772084] [Find markers #24 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772084 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772084 --iAnnot /col_attrs/Clustering_Leiden_resolution_0.4__default__302_ --id 470560 --is_count_table true  1> $PROJECT_DIR/markers/772084/exec.out 2> $PROJECT_DIR/markers/772084/exec.err'"


## ----------------------------------------------------------------
## Run 772085  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/772085/"

## Running Find markers [772085] [Find markers #25 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772085] [Find markers #25 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772085 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772085 --iAnnot /col_attrs/Clustering_Leiden_resolution_0.4__default__302_ --id 470560 --is_count_table true  1> $PROJECT_DIR/markers/772085/exec.out 2> $PROJECT_DIR/markers/772085/exec.err'"


## ----------------------------------------------------------------
## Run 772086  Find markers  (Find markers #26 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/772086/"

## Running Find markers [772086] [Find markers #26 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772086] [Find markers #26 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772086 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772086 --iAnnot /col_attrs/Clustering_Leiden_resolution_0.6 --id 470568 --is_count_table true  1> $PROJECT_DIR/markers/772086/exec.out 2> $PROJECT_DIR/markers/772086/exec.err'"


## ----------------------------------------------------------------
## Run 772087  Find markers  (Find markers #27 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/772087/"

## Running Find markers [772087] [Find markers #27 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772087] [Find markers #27 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772087 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772087 --iAnnot /col_attrs/Clustering_Leiden_resolution_0.8__14_ --id 470530 --is_count_table true  1> $PROJECT_DIR/markers/772087/exec.out 2> $PROJECT_DIR/markers/772087/exec.err'"


## ----------------------------------------------------------------
## Run 772088  Find markers  (Find markers #28 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/772088/"

## Running Find markers [772088] [Find markers #28 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772088] [Find markers #28 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772088 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772088 --iAnnot /col_attrs/Clustering_Leiden_resolution_10.0 --id 470544 --is_count_table true  1> $PROJECT_DIR/markers/772088/exec.out 2> $PROJECT_DIR/markers/772088/exec.err'"


## ----------------------------------------------------------------
## Run 772089  Find markers  (Find markers #29 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/772089/"

## Running Find markers [772089] [Find markers #29 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772089] [Find markers #29 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772089 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772089 --iAnnot /col_attrs/Clustering_Leiden_resolution_1.0__18_ --id 470549 --is_count_table true  1> $PROJECT_DIR/markers/772089/exec.out 2> $PROJECT_DIR/markers/772089/exec.err'"


## ----------------------------------------------------------------
## Run 772090  Find markers  (Find markers #30 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/772090/"

## Running Find markers [772090] [Find markers #30 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772090] [Find markers #30 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772090 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772090 --iAnnot /col_attrs/Clustering_Leiden_resolution_0.8__14_ --id 470530 --is_count_table true  1> $PROJECT_DIR/markers/772090/exec.out 2> $PROJECT_DIR/markers/772090/exec.err'"


## ----------------------------------------------------------------
## Run 772091  Find markers  (Find markers #31 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/772091/"

## Running Find markers [772091] [Find markers #31 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [772091] [Find markers #31 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_772091 --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 $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/772091 --iAnnot /col_attrs/sex --id 470565 --is_count_table true  1> $PROJECT_DIR/markers/772091/exec.out 2> $PROJECT_DIR/markers/772091/exec.err'"