## This script contains all commands executed in the PROJECT vitm3b and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT vitm3b / ASAP97**********************'
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/vitm3b
## 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/de/ && mkdir -p $PROJECT_DIR/ge/ && 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/vitm3b/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 709773  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/709773/"

## Running Normalization [709773] [Normalization #1 asap_seurat] (input_matrix:parsing)
echo '-> Running Normalization [709773] [Normalization #1 asap_seurat] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709773 --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/vitm3b/parsing/output.loom -o /data/asap2/users/1465/vitm3b/normalization/709773/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1465/vitm3b/normalization/709773/exec.out 2> /data/asap2/users/1465/vitm3b/normalization/709773/exec.err'"


## ----------------------------------------------------------------
## Run 709774  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/709774/"

## Running Find markers [709774] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [709774] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709774 --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/vitm3b/parsing/output.loom -o /data/asap2/users/1465/vitm3b/markers/709774 --iAnnot /col_attrs/annotation --id 468591  1> /data/asap2/users/1465/vitm3b/markers/709774/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709774/exec.err'"


## ----------------------------------------------------------------
## Run 709775  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/709775/"

## Running Find markers [709775] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [709775] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709775 --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/vitm3b/parsing/output.loom -o /data/asap2/users/1465/vitm3b/markers/709775 --iAnnot /col_attrs/annotation --id 468591  1> /data/asap2/users/1465/vitm3b/markers/709775/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709775/exec.err'"


## ----------------------------------------------------------------
## Run 709776  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/709776/"

## Running Find markers [709776] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [709776] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709776 --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/vitm3b/parsing/output.loom -o /data/asap2/users/1465/vitm3b/markers/709776 --iAnnot /col_attrs/annotation --id 468591  1> /data/asap2/users/1465/vitm3b/markers/709776/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709776/exec.err'"


## ----------------------------------------------------------------
## Run 709777  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/709777/"

## Running Find markers [709777] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [709777] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709777 --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/vitm3b/parsing/output.loom -o /data/asap2/users/1465/vitm3b/markers/709777 --iAnnot /col_attrs/annotation --id 468591  1> /data/asap2/users/1465/vitm3b/markers/709777/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709777/exec.err'"


## ----------------------------------------------------------------
## Run 709778  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/709778/"

## Running Marker enrichment [709778] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [709778] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709778 --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/1465/vitm3b/markers/709776 -o /data/asap2/users/1465/vitm3b/markers/709778 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/markers/709778/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709778/exec.err'"


## ----------------------------------------------------------------
## Run 709779  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/709779/"

## Running Marker enrichment [709779] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [709779] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709779 --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/1465/vitm3b/markers/709777 -o /data/asap2/users/1465/vitm3b/markers/709779 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/markers/709779/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709779/exec.err'"


## ----------------------------------------------------------------
## Run 709780  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/709780/"

## Running Marker enrichment [709780] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [709780] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709780 --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/1465/vitm3b/markers/709774 -o /data/asap2/users/1465/vitm3b/markers/709780 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/markers/709780/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709780/exec.err'"


## ----------------------------------------------------------------
## Run 709781  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/709781/"

## Running Marker enrichment [709781] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [709781] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709781 --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/1465/vitm3b/markers/709775 -o /data/asap2/users/1465/vitm3b/markers/709781 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/markers/709781/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709781/exec.err'"


## ----------------------------------------------------------------
## Run 709782  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/709782/"

## Running Find markers [709782] [Find markers #2 asap_markers] ()
echo '-> Running Find markers [709782] [Find markers #2 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709782 --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/vitm3b/parsing/output.loom -o /data/asap2/users/1465/vitm3b/markers/709782 --iAnnot /col_attrs/note --id 468572 --is_count_table  1> /data/asap2/users/1465/vitm3b/markers/709782/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709782/exec.err'"


## ----------------------------------------------------------------
## Run 709783  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/709783/"

## Running Marker enrichment [709783] [Marker enrichment #3 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [709783] [Marker enrichment #3 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709783 --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/1465/vitm3b/markers/709782 -o /data/asap2/users/1465/vitm3b/markers/709783 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/markers/709783/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709783/exec.err'"


## ----------------------------------------------------------------
## Run 709784  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/709784/"

## Running Find markers [709784] [Find markers #3 asap_markers] ()
echo '-> Running Find markers [709784] [Find markers #3 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709784 --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/vitm3b/parsing/output.loom -o /data/asap2/users/1465/vitm3b/markers/709784 --iAnnot /col_attrs/Clustering_Annotation --id 468580 --is_count_table  1> /data/asap2/users/1465/vitm3b/markers/709784/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709784/exec.err'"


## ----------------------------------------------------------------
## Run 709785  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/709785/"

## Running Marker enrichment [709785] [Marker enrichment #4 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [709785] [Marker enrichment #4 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709785 --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/1465/vitm3b/markers/709784 -o /data/asap2/users/1465/vitm3b/markers/709785 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/markers/709785/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709785/exec.err'"


## ----------------------------------------------------------------
## Run 709786  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/709786/"

## Running Find markers [709786] [Find markers #4 asap_markers] ()
echo '-> Running Find markers [709786] [Find markers #4 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709786 --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/vitm3b/parsing/output.loom -o /data/asap2/users/1465/vitm3b/markers/709786 --iAnnot /col_attrs/sex --id 468606 --is_count_table  1> /data/asap2/users/1465/vitm3b/markers/709786/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709786/exec.err'"


## ----------------------------------------------------------------
## Run 709787  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/709787/"

## Running Marker enrichment [709787] [Marker enrichment #5 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [709787] [Marker enrichment #5 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709787 --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/1465/vitm3b/markers/709786 -o /data/asap2/users/1465/vitm3b/markers/709787 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/markers/709787/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709787/exec.err'"


## ----------------------------------------------------------------
## Run 709788  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/709788/"

## Running Find markers [709788] [Find markers #5 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [709788] [Find markers #5 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709788 --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/vitm3b/parsing/output.loom -o /data/asap2/users/1465/vitm3b/markers/709788 --iAnnot /col_attrs/annotation --id 468591 --is_count_table true  1> /data/asap2/users/1465/vitm3b/markers/709788/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709788/exec.err'"


## ----------------------------------------------------------------
## Run 709789  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/709789/"

## Running Marker enrichment [709789] [Marker enrichment #6 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [709789] [Marker enrichment #6 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709789 --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/1465/vitm3b/markers/709788 -o /data/asap2/users/1465/vitm3b/markers/709789 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/markers/709789/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709789/exec.err'"


## ----------------------------------------------------------------
## Run 709790  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/709790/"

## Running Find markers [709790] [Find markers #6 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [709790] [Find markers #6 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709790 --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/vitm3b/parsing/output.loom -o /data/asap2/users/1465/vitm3b/markers/709790 --iAnnot /col_attrs/batch --id 468573 --is_count_table true  1> /data/asap2/users/1465/vitm3b/markers/709790/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709790/exec.err'"


## ----------------------------------------------------------------
## Run 709791  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/709791/"

## Running Find markers [709791] [Find markers #7 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [709791] [Find markers #7 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709791 --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/vitm3b/parsing/output.loom -o /data/asap2/users/1465/vitm3b/markers/709791 --iAnnot /col_attrs/Clustering_Annotation --id 468580 --is_count_table true  1> /data/asap2/users/1465/vitm3b/markers/709791/exec.out 2> /data/asap2/users/1465/vitm3b/markers/709791/exec.err'"


## ----------------------------------------------------------------
## Run 709792  Differential expression  (Differential expression #1 wilcox_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/de/709792/"

## Running Differential expression [709792] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:parsing group_ref:0 group_comp: min_pct:0.25 fc_threshold:1)
echo '-> Running Differential expression [709792] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:parsing group_ref:0 group_comp: min_pct:0.25 fc_threshold:1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709792 --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 'Rscript --vanilla de.R  /data/asap2/users/1465/vitm3b/parsing/output.loom /data/asap2/users/1465/vitm3b/de/709792 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_1_wilcox_seurat null /col_attrs/Clustering_Annotation 0 null false 0.25 null 1 null 16 1> /data/asap2/users/1465/vitm3b/de/709792/exec.out 2> /data/asap2/users/1465/vitm3b/de/709792/exec.err'"


## ----------------------------------------------------------------
## Run 709793  Gene Enrichment  (Gene Enrichment #1 basic)
## ----------------------------------------------------------------

## 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/ge/709793/"

## Running Gene Enrichment [709793] [Gene Enrichment #1 basic] (input_de:de #1 min:10)
echo '-> Running Gene Enrichment [709793] [Gene Enrichment #1 basic] (input_de:de #1 min:10)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709793 --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 Enrichment -loom /data/asap2/users/1465/vitm3b/parsing/output.loom -m fet -f /data/asap2/users/1465/vitm3b/tmp/1465_709792_2_0.05_filtered_ids.json -o /data/asap2/users/1465/vitm3b/ge/709793/output.json -max 500 -min 10 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/ge/709793/exec.out 2> /data/asap2/users/1465/vitm3b/ge/709793/exec.err'"


## ----------------------------------------------------------------
## Run 709794  Gene Enrichment  (Gene Enrichment #2 basic)
## ----------------------------------------------------------------

## 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/ge/709794/"

## Running Gene Enrichment [709794] [Gene Enrichment #2 basic] (input_de:de #1 min:10)
echo '-> Running Gene Enrichment [709794] [Gene Enrichment #2 basic] (input_de:de #1 min:10)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709794 --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 Enrichment -loom /data/asap2/users/1465/vitm3b/parsing/output.loom -m fet -f /data/asap2/users/1465/vitm3b/tmp/1465_709792_2_0.05_filtered_ids.json -o /data/asap2/users/1465/vitm3b/ge/709794/output.json -max 500 -min 10 -adj fdr -geneset 672 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/ge/709794/exec.out 2> /data/asap2/users/1465/vitm3b/ge/709794/exec.err'"


## ----------------------------------------------------------------
## Run 709795  Gene Enrichment  (Gene Enrichment #3 basic)
## ----------------------------------------------------------------

## 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/ge/709795/"

## Running Gene Enrichment [709795] [Gene Enrichment #3 basic] (input_de:de #1 min:10)
echo '-> Running Gene Enrichment [709795] [Gene Enrichment #3 basic] (input_de:de #1 min:10)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709795 --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 Enrichment -loom /data/asap2/users/1465/vitm3b/parsing/output.loom -m fet -f /data/asap2/users/1465/vitm3b/tmp/1465_709792_2_0.05_filtered_ids.json -o /data/asap2/users/1465/vitm3b/ge/709795/output.json -max 500 -min 10 -adj fdr -geneset 673 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/ge/709795/exec.out 2> /data/asap2/users/1465/vitm3b/ge/709795/exec.err'"


## ----------------------------------------------------------------
## Run 709796  Gene Enrichment  (Gene Enrichment #4 basic)
## ----------------------------------------------------------------

## 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/ge/709796/"

## Running Gene Enrichment [709796] [Gene Enrichment #4 basic] (input_de:de #1 min:10)
echo '-> Running Gene Enrichment [709796] [Gene Enrichment #4 basic] (input_de:de #1 min:10)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709796 --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 Enrichment -loom /data/asap2/users/1465/vitm3b/parsing/output.loom -m fet -f /data/asap2/users/1465/vitm3b/tmp/1465_709792_2_0.05_filtered_ids.json -o /data/asap2/users/1465/vitm3b/ge/709796/output.json -max 500 -min 10 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/ge/709796/exec.out 2> /data/asap2/users/1465/vitm3b/ge/709796/exec.err'"


## ----------------------------------------------------------------
## Run 709797  Gene Enrichment  (Gene Enrichment #5 basic)
## ----------------------------------------------------------------

## 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/ge/709797/"

## Running Gene Enrichment [709797] [Gene Enrichment #5 basic] (input_de:de #1 min:10)
echo '-> Running Gene Enrichment [709797] [Gene Enrichment #5 basic] (input_de:de #1 min:10)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_709797 --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 Enrichment -loom /data/asap2/users/1465/vitm3b/parsing/output.loom -m fet -f /data/asap2/users/1465/vitm3b/tmp/1465_709792_2_0.05_filtered_ids.json -o /data/asap2/users/1465/vitm3b/ge/709797/output.json -max 500 -min 10 -adj fdr -geneset 3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1465/vitm3b/ge/709797/exec.out 2> /data/asap2/users/1465/vitm3b/ge/709797/exec.err'"