## This script contains all commands executed in the PROJECT o0fa1d and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT o0fa1d / ASAP42**********************'
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/o0fa1d
## 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/o0fa1d/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 73639  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/73639/"

## Running Normalization [73639] [Normalization #1 asap_seurat] (input_matrix:parsing scale_factor:10000)
echo '-> Running Normalization [73639] [Normalization #1 asap_seurat] (input_matrix:parsing scale_factor:10000)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_73639 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/normalization/73639/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/o0fa1d/normalization/73639/exec.out 2> /data/asap2/users/1/o0fa1d/normalization/73639/exec.err'"


## ----------------------------------------------------------------
## Run 153888  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/153888/"

## Running Find markers [153888] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [153888] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_153888 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/153888 --iAnnot /col_attrs/annotation --id 468591  1> /data/asap2/users/1/o0fa1d/markers/153888/exec.out 2> /data/asap2/users/1/o0fa1d/markers/153888/exec.err'"


## ----------------------------------------------------------------
## Run 153889  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/153889/"

## Running Find markers [153889] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [153889] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_153889 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/153889 --iAnnot /col_attrs/annotation --id 468591  1> /data/asap2/users/1/o0fa1d/markers/153889/exec.out 2> /data/asap2/users/1/o0fa1d/markers/153889/exec.err'"


## ----------------------------------------------------------------
## Run 153890  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/153890/"

## Running Find markers [153890] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [153890] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_153890 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/153890 --iAnnot /col_attrs/annotation --id 468591  1> /data/asap2/users/1/o0fa1d/markers/153890/exec.out 2> /data/asap2/users/1/o0fa1d/markers/153890/exec.err'"


## ----------------------------------------------------------------
## Run 153891  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/153891/"

## Running Find markers [153891] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [153891] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_153891 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/153891 --iAnnot /col_attrs/annotation --id 468591  1> /data/asap2/users/1/o0fa1d/markers/153891/exec.out 2> /data/asap2/users/1/o0fa1d/markers/153891/exec.err'"


## ----------------------------------------------------------------
## Run 153892  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/153892/"

## Running Marker enrichment [153892] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [153892] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_153892 --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/o0fa1d/markers/153890 -o /data/asap2/users/1/o0fa1d/markers/153892 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/o0fa1d/markers/153892/exec.out 2> /data/asap2/users/1/o0fa1d/markers/153892/exec.err'"


## ----------------------------------------------------------------
## Run 153893  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/153893/"

## Running Marker enrichment [153893] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [153893] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_153893 --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/o0fa1d/markers/153891 -o /data/asap2/users/1/o0fa1d/markers/153893 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/o0fa1d/markers/153893/exec.out 2> /data/asap2/users/1/o0fa1d/markers/153893/exec.err'"


## ----------------------------------------------------------------
## Run 153894  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/153894/"

## Running Marker enrichment [153894] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [153894] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_153894 --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/o0fa1d/markers/153888 -o /data/asap2/users/1/o0fa1d/markers/153894 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/o0fa1d/markers/153894/exec.out 2> /data/asap2/users/1/o0fa1d/markers/153894/exec.err'"


## ----------------------------------------------------------------
## Run 153895  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/153895/"

## Running Marker enrichment [153895] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [153895] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_153895 --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/o0fa1d/markers/153889 -o /data/asap2/users/1/o0fa1d/markers/153895 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/o0fa1d/markers/153895/exec.out 2> /data/asap2/users/1/o0fa1d/markers/153895/exec.err'"


## ----------------------------------------------------------------
## Run 286165  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/286165/"

## Running Find markers [286165] [Find markers #2 asap_markers] ()
echo '-> Running Find markers [286165] [Find markers #2 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_286165 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/286165 --iAnnot /col_attrs/note --id 468572 --is_count_table   1> /data/asap2/users/1/o0fa1d/markers/286165/exec.out 2> /data/asap2/users/1/o0fa1d/markers/286165/exec.err'"


## ----------------------------------------------------------------
## Run 286166  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/286166/"

## Running Marker enrichment [286166] [Marker enrichment #3 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [286166] [Marker enrichment #3 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_286166 --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/o0fa1d/markers/286165 -o /data/asap2/users/1/o0fa1d/markers/286166 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/o0fa1d/markers/286166/exec.out 2> /data/asap2/users/1/o0fa1d/markers/286166/exec.err'"


## ----------------------------------------------------------------
## Run 286167  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/286167/"

## Running Find markers [286167] [Find markers #3 asap_markers] ()
echo '-> Running Find markers [286167] [Find markers #3 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_286167 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/286167 --iAnnot /col_attrs/Clustering_Annotation --id 468580 --is_count_table   1> /data/asap2/users/1/o0fa1d/markers/286167/exec.out 2> /data/asap2/users/1/o0fa1d/markers/286167/exec.err'"


## ----------------------------------------------------------------
## Run 286168  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/286168/"

## Running Marker enrichment [286168] [Marker enrichment #4 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [286168] [Marker enrichment #4 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_286168 --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/o0fa1d/markers/286167 -o /data/asap2/users/1/o0fa1d/markers/286168 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/o0fa1d/markers/286168/exec.out 2> /data/asap2/users/1/o0fa1d/markers/286168/exec.err'"


## ----------------------------------------------------------------
## Run 300755  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/300755/"

## Running Find markers [300755] [Find markers #4 asap_markers] ()
echo '-> Running Find markers [300755] [Find markers #4 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_300755 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/300755 --iAnnot /col_attrs/sex --id 468606 --is_count_table   1> /data/asap2/users/1/o0fa1d/markers/300755/exec.out 2> /data/asap2/users/1/o0fa1d/markers/300755/exec.err'"


## ----------------------------------------------------------------
## Run 300756  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/300756/"

## Running Marker enrichment [300756] [Marker enrichment #5 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [300756] [Marker enrichment #5 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_300756 --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/o0fa1d/markers/300755 -o /data/asap2/users/1/o0fa1d/markers/300756 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/o0fa1d/markers/300756/exec.out 2> /data/asap2/users/1/o0fa1d/markers/300756/exec.err'"


## ----------------------------------------------------------------
## Run 343098  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/343098/"

## Running Find markers [343098] [Find markers #5 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [343098] [Find markers #5 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_343098 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/343098 --iAnnot /col_attrs/annotation --id 468591 --is_count_table true  1> /data/asap2/users/1/o0fa1d/markers/343098/exec.out 2> /data/asap2/users/1/o0fa1d/markers/343098/exec.err'"


## ----------------------------------------------------------------
## Run 343099  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/343099/"

## Running Marker enrichment [343099] [Marker enrichment #6 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [343099] [Marker enrichment #6 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_343099 --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/o0fa1d/markers/343098 -o /data/asap2/users/1/o0fa1d/markers/343099 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/o0fa1d/markers/343099/exec.out 2> /data/asap2/users/1/o0fa1d/markers/343099/exec.err'"


## ----------------------------------------------------------------
## Run 536947  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/536947/"

## Running Find markers [536947] [Find markers #6 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [536947] [Find markers #6 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_536947 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/536947 --iAnnot /col_attrs/batch --id 468573 --is_count_table true  1> /data/asap2/users/1/o0fa1d/markers/536947/exec.out 2> /data/asap2/users/1/o0fa1d/markers/536947/exec.err'"


## ----------------------------------------------------------------
## Run 558383  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/558383/"

## Running Find markers [558383] [Find markers #7 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [558383] [Find markers #7 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_558383 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/558383 --iAnnot /col_attrs/Clustering_Annotation --id 468580 --is_count_table true  1> /data/asap2/users/1/o0fa1d/markers/558383/exec.out 2> /data/asap2/users/1/o0fa1d/markers/558383/exec.err'"


## ----------------------------------------------------------------
## Run 711338  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/711338/"

## Running Find markers [711338] [Find markers #8 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [711338] [Find markers #8 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_711338 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/711338 --iAnnot /col_attrs/annotation__ontology_id --id 468552 --is_count_table true  1> /data/asap2/users/1/o0fa1d/markers/711338/exec.out 2> /data/asap2/users/1/o0fa1d/markers/711338/exec.err'"


## ----------------------------------------------------------------
## Run 754486  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/754486/"

## Running Find markers [754486] [Find markers #9 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [754486] [Find markers #9 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_754486 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/754486 --iAnnot /col_attrs/age --id 468561 --is_count_table true  1> /data/asap2/users/1/o0fa1d/markers/754486/exec.out 2> /data/asap2/users/1/o0fa1d/markers/754486/exec.err'"


## ----------------------------------------------------------------
## Run 754487  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/754487/"

## Running Find markers [754487] [Find markers #10 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [754487] [Find markers #10 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_754487 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/754487 --iAnnot /col_attrs/R_annotation_broad__ontology_id --id 468611 --is_count_table true  1> /data/asap2/users/1/o0fa1d/markers/754487/exec.out 2> /data/asap2/users/1/o0fa1d/markers/754487/exec.err'"


## ----------------------------------------------------------------
## Run 754488  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/754488/"

## Running Find markers [754488] [Find markers #11 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [754488] [Find markers #11 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_754488 --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/o0fa1d/parsing/output.loom -o /data/asap2/users/1/o0fa1d/markers/754488 --iAnnot /col_attrs/Clustering_Annotation__Relaxed_ --id 468553 --is_count_table true  1> /data/asap2/users/1/o0fa1d/markers/754488/exec.out 2> /data/asap2/users/1/o0fa1d/markers/754488/exec.err'"