## This script contains all commands executed in the PROJECT lb9jni and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT lb9jni / ASAP22**********************'
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/lb9jni
## 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/lb9jni/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 73705  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/73705/"

## Running Normalization [73705] [Normalization #1 asap_seurat] (input_matrix:parsing)
echo '-> Running Normalization [73705] [Normalization #1 asap_seurat] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_73705 --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/lb9jni/parsing/output.loom -o /data/asap2/users/1/lb9jni/normalization/73705/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/lb9jni/normalization/73705/exec.out 2> /data/asap2/users/1/lb9jni/normalization/73705/exec.err'"


## ----------------------------------------------------------------
## Run 137545  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/137545/"

## Running Find markers [137545] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [137545] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_137545 --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/lb9jni/parsing/output.loom -o /data/asap2/users/1/lb9jni/markers/137545 --iAnnot /col_attrs/Clustering_Leiden_resolution_1.6__default__233_ --id 471492  1> /data/asap2/users/1/lb9jni/markers/137545/exec.out 2> /data/asap2/users/1/lb9jni/markers/137545/exec.err'"


## ----------------------------------------------------------------
## Run 137546  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/137546/"

## Running Marker enrichment [137546] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [137546] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_137546 --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/lb9jni/markers/137545 -o /data/asap2/users/1/lb9jni/markers/137546 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/lb9jni/markers/137546/exec.out 2> /data/asap2/users/1/lb9jni/markers/137546/exec.err'"


## ----------------------------------------------------------------
## Run 142168  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/142168/"

## Running Find markers [142168] [Find markers #2 asap_markers] ()
echo '-> Running Find markers [142168] [Find markers #2 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_142168 --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/lb9jni/parsing/output.loom -o /data/asap2/users/1/lb9jni/markers/142168 --iAnnot /col_attrs/annotation_broad --id 471458  1> /data/asap2/users/1/lb9jni/markers/142168/exec.out 2> /data/asap2/users/1/lb9jni/markers/142168/exec.err'"


## ----------------------------------------------------------------
## Run 142169  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/142169/"

## Running Marker enrichment [142169] [Marker enrichment #3 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [142169] [Marker enrichment #3 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_142169 --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/lb9jni/markers/142168 -o /data/asap2/users/1/lb9jni/markers/142169 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/lb9jni/markers/142169/exec.out 2> /data/asap2/users/1/lb9jni/markers/142169/exec.err'"


## ----------------------------------------------------------------
## Run 142171  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/142171/"

## Running Find markers [142171] [Find markers #3 asap_markers] ()
echo '-> Running Find markers [142171] [Find markers #3 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_142171 --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/lb9jni/parsing/output.loom -o /data/asap2/users/1/lb9jni/markers/142171 --iAnnot /col_attrs/Clustering_Annotation --id 471484  1> /data/asap2/users/1/lb9jni/markers/142171/exec.out 2> /data/asap2/users/1/lb9jni/markers/142171/exec.err'"


## ----------------------------------------------------------------
## Run 142172  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/142172/"

## Running Marker enrichment [142172] [Marker enrichment #4 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [142172] [Marker enrichment #4 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_142172 --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/lb9jni/markers/142171 -o /data/asap2/users/1/lb9jni/markers/142172 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/lb9jni/markers/142172/exec.out 2> /data/asap2/users/1/lb9jni/markers/142172/exec.err'"


## ----------------------------------------------------------------
## Run 195004  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/195004/"

## Running Find markers [195004] [Find markers #4 asap_markers] ()
echo '-> Running Find markers [195004] [Find markers #4 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_195004 --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/lb9jni/parsing/output.loom -o /data/asap2/users/1/lb9jni/markers/195004 --iAnnot /col_attrs/annotation --id 471494  1> /data/asap2/users/1/lb9jni/markers/195004/exec.out 2> /data/asap2/users/1/lb9jni/markers/195004/exec.err'"


## ----------------------------------------------------------------
## Run 195005  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/195005/"

## Running Marker enrichment [195005] [Marker enrichment #5 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [195005] [Marker enrichment #5 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_195005 --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/lb9jni/markers/195004 -o /data/asap2/users/1/lb9jni/markers/195005 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/lb9jni/markers/195005/exec.out 2> /data/asap2/users/1/lb9jni/markers/195005/exec.err'"


## ----------------------------------------------------------------
## Run 255508  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/255508/"

## Running Find markers [255508] [Find markers #5 asap_markers] ()
echo '-> Running Find markers [255508] [Find markers #5 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_255508 --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/lb9jni/parsing/output.loom -o /data/asap2/users/1/lb9jni/markers/255508 --iAnnot /col_attrs/annotation__ontology_id --id 471456 --is_count_table  1> /data/asap2/users/1/lb9jni/markers/255508/exec.out 2> /data/asap2/users/1/lb9jni/markers/255508/exec.err'"


## ----------------------------------------------------------------
## Run 255509  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/255509/"

## Running Marker enrichment [255509] [Marker enrichment #6 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [255509] [Marker enrichment #6 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_255509 --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/lb9jni/markers/255508 -o /data/asap2/users/1/lb9jni/markers/255509 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/lb9jni/markers/255509/exec.out 2> /data/asap2/users/1/lb9jni/markers/255509/exec.err'"


## ----------------------------------------------------------------
## Run 342428  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/342428/"

## Running Find markers [342428] [Find markers #6 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [342428] [Find markers #6 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_342428 --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/lb9jni/parsing/output.loom -o /data/asap2/users/1/lb9jni/markers/342428 --iAnnot /col_attrs/annotation_broad --id 471458 --is_count_table true  1> /data/asap2/users/1/lb9jni/markers/342428/exec.out 2> /data/asap2/users/1/lb9jni/markers/342428/exec.err'"


## ----------------------------------------------------------------
## Run 342429  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/342429/"

## Running Marker enrichment [342429] [Marker enrichment #7 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [342429] [Marker enrichment #7 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_342429 --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/lb9jni/markers/342428 -o /data/asap2/users/1/lb9jni/markers/342429 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/lb9jni/markers/342429/exec.out 2> /data/asap2/users/1/lb9jni/markers/342429/exec.err'"


## ----------------------------------------------------------------
## Run 388093  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/388093/"

## Running Find markers [388093] [Find markers #7 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [388093] [Find markers #7 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_388093 --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/lb9jni/parsing/output.loom -o /data/asap2/users/1/lb9jni/markers/388093 --iAnnot /col_attrs/tissue --id 471490 --is_count_table true  1> /data/asap2/users/1/lb9jni/markers/388093/exec.out 2> /data/asap2/users/1/lb9jni/markers/388093/exec.err'"


## ----------------------------------------------------------------
## Run 388094  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/388094/"

## Running Marker enrichment [388094] [Marker enrichment #8 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [388094] [Marker enrichment #8 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_388094 --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/lb9jni/markers/388093 -o /data/asap2/users/1/lb9jni/markers/388094 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/lb9jni/markers/388094/exec.out 2> /data/asap2/users/1/lb9jni/markers/388094/exec.err'"


## ----------------------------------------------------------------
## Run 561772  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/561772/"

## Running Find markers [561772] [Find markers #8 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [561772] [Find markers #8 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_561772 --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/lb9jni/parsing/output.loom -o /data/asap2/users/1/lb9jni/markers/561772 --iAnnot /col_attrs/annotation --id 471494 --is_count_table true  1> /data/asap2/users/1/lb9jni/markers/561772/exec.out 2> /data/asap2/users/1/lb9jni/markers/561772/exec.err'"


## ----------------------------------------------------------------
## Run 753769  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/753769/"

## Running Find markers [753769] [Find markers #9 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [753769] [Find markers #9 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_753769 --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/lb9jni/parsing/output.loom -o /data/asap2/users/1/lb9jni/markers/753769 --iAnnot /col_attrs/age --id 471466 --is_count_table true  1> /data/asap2/users/1/lb9jni/markers/753769/exec.out 2> /data/asap2/users/1/lb9jni/markers/753769/exec.err'"