## This script contains all commands executed in the PROJECT qxj5ei and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT qxj5ei / ASAP55**********************'
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/qxj5ei
## 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/qxj5ei/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 73661  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/73661/"

## Running Normalization [73661] [Normalization #1 asap_seurat] (input_matrix:parsing)
echo '-> Running Normalization [73661] [Normalization #1 asap_seurat] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_73661 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/normalization/73661/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/qxj5ei/normalization/73661/exec.out 2> /data/asap2/users/1/qxj5ei/normalization/73661/exec.err'"


## ----------------------------------------------------------------
## Run 171423  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/171423/"

## Running Find markers [171423] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [171423] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_171423 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/171423 --iAnnot /col_attrs/annotation --id 469594  1> /data/asap2/users/1/qxj5ei/markers/171423/exec.out 2> /data/asap2/users/1/qxj5ei/markers/171423/exec.err'"


## ----------------------------------------------------------------
## Run 171424  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/171424/"

## Running Marker enrichment [171424] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [171424] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_171424 --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/qxj5ei/markers/171423 -o /data/asap2/users/1/qxj5ei/markers/171424 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/qxj5ei/markers/171424/exec.out 2> /data/asap2/users/1/qxj5ei/markers/171424/exec.err'"


## ----------------------------------------------------------------
## Run 279159  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/279159/"

## Running Find markers [279159] [Find markers #2 asap_markers] ()
echo '-> Running Find markers [279159] [Find markers #2 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_279159 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/279159 --iAnnot /col_attrs/R_annotation --id 469613 --is_count_table  1> /data/asap2/users/1/qxj5ei/markers/279159/exec.out 2> /data/asap2/users/1/qxj5ei/markers/279159/exec.err'"


## ----------------------------------------------------------------
## Run 279160  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/279160/"

## Running Marker enrichment [279160] [Marker enrichment #3 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [279160] [Marker enrichment #3 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_279160 --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/qxj5ei/markers/279159 -o /data/asap2/users/1/qxj5ei/markers/279160 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/qxj5ei/markers/279160/exec.out 2> /data/asap2/users/1/qxj5ei/markers/279160/exec.err'"


## ----------------------------------------------------------------
## Run 302772  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/302772/"

## Running Find markers [302772] [Find markers #3 asap_markers] ()
echo '-> Running Find markers [302772] [Find markers #3 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_302772 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/302772 --iAnnot /col_attrs/ClusterID --id 469561 --is_count_table  1> /data/asap2/users/1/qxj5ei/markers/302772/exec.out 2> /data/asap2/users/1/qxj5ei/markers/302772/exec.err'"


## ----------------------------------------------------------------
## Run 302773  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/302773/"

## Running Marker enrichment [302773] [Marker enrichment #4 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [302773] [Marker enrichment #4 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_302773 --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/qxj5ei/markers/302772 -o /data/asap2/users/1/qxj5ei/markers/302773 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/qxj5ei/markers/302773/exec.out 2> /data/asap2/users/1/qxj5ei/markers/302773/exec.err'"


## ----------------------------------------------------------------
## Run 350665  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/350665/"

## Running Find markers [350665] [Find markers #4 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [350665] [Find markers #4 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_350665 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/350665 --iAnnot /col_attrs/annotation --id 469594 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/350665/exec.out 2> /data/asap2/users/1/qxj5ei/markers/350665/exec.err'"


## ----------------------------------------------------------------
## Run 350666  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/350666/"

## Running Marker enrichment [350666] [Marker enrichment #5 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [350666] [Marker enrichment #5 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_350666 --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/qxj5ei/markers/350665 -o /data/asap2/users/1/qxj5ei/markers/350666 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/qxj5ei/markers/350666/exec.out 2> /data/asap2/users/1/qxj5ei/markers/350666/exec.err'"


## ----------------------------------------------------------------
## Run 359487  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/359487/"

## Running Find markers [359487] [Find markers #5 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [359487] [Find markers #5 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_359487 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/359487 --iAnnot /col_attrs/tissue --id 469588 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/359487/exec.out 2> /data/asap2/users/1/qxj5ei/markers/359487/exec.err'"


## ----------------------------------------------------------------
## Run 359488  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/359488/"

## Running Marker enrichment [359488] [Marker enrichment #6 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [359488] [Marker enrichment #6 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_359488 --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/qxj5ei/markers/359487 -o /data/asap2/users/1/qxj5ei/markers/359488 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/qxj5ei/markers/359488/exec.out 2> /data/asap2/users/1/qxj5ei/markers/359488/exec.err'"


## ----------------------------------------------------------------
## Run 420011  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/420011/"

## Running Find markers [420011] [Find markers #6 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [420011] [Find markers #6 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_420011 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/420011 --iAnnot /col_attrs/annotation__ontology_id --id 469556 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/420011/exec.out 2> /data/asap2/users/1/qxj5ei/markers/420011/exec.err'"


## ----------------------------------------------------------------
## Run 420012  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/420012/"

## Running Marker enrichment [420012] [Marker enrichment #7 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [420012] [Marker enrichment #7 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_420012 --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/qxj5ei/markers/420011 -o /data/asap2/users/1/qxj5ei/markers/420012 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/qxj5ei/markers/420012/exec.out 2> /data/asap2/users/1/qxj5ei/markers/420012/exec.err'"


## ----------------------------------------------------------------
## Run 451280  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/451280/"

## Running Find markers [451280] [Find markers #7 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [451280] [Find markers #7 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_451280 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/451280 --iAnnot /col_attrs/annotation_broad --id 469560 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/451280/exec.out 2> /data/asap2/users/1/qxj5ei/markers/451280/exec.err'"


## ----------------------------------------------------------------
## Run 553233  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/553233/"

## Running Find markers [553233] [Find markers #8 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [553233] [Find markers #8 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_553233 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/553233 --iAnnot /col_attrs/scrublet__predicted_doublets_based_on_10x_chromium_spec --id 469563 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/553233/exec.out 2> /data/asap2/users/1/qxj5ei/markers/553233/exec.err'"


## ----------------------------------------------------------------
## Run 650369  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/650369/"

## Running Find markers [650369] [Find markers #9 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [650369] [Find markers #9 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_650369 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/650369 --iAnnot /col_attrs/fly_genetics --id 469574 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/650369/exec.out 2> /data/asap2/users/1/qxj5ei/markers/650369/exec.err'"


## ----------------------------------------------------------------
## Run 650370  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/650370/"

## Running Find markers [650370] [Find markers #10 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [650370] [Find markers #10 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_650370 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/650370 --iAnnot /col_attrs/annotation_broad_extrapolated__ontology_id --id 469582 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/650370/exec.out 2> /data/asap2/users/1/qxj5ei/markers/650370/exec.err'"


## ----------------------------------------------------------------
## Run 685474  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/685474/"

## Running Find markers [685474] [Find markers #11 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [685474] [Find markers #11 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_685474 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/685474 --iAnnot /col_attrs/Clustering_Broad_Annotation --id 469619 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/685474/exec.out 2> /data/asap2/users/1/qxj5ei/markers/685474/exec.err'"


## ----------------------------------------------------------------
## Run 701371  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/701371/"

## Running Find markers [701371] [Find markers #12 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [701371] [Find markers #12 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_701371 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/701371 --iAnnot /col_attrs/ClusterID --id 469561 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/701371/exec.out 2> /data/asap2/users/1/qxj5ei/markers/701371/exec.err'"


## ----------------------------------------------------------------
## Run 701372  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/701372/"

## Running Find markers [701372] [Find markers #13 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [701372] [Find markers #13 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_701372 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/701372 --iAnnot /col_attrs/batch_id --id 469607 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/701372/exec.out 2> /data/asap2/users/1/qxj5ei/markers/701372/exec.err'"


## ----------------------------------------------------------------
## Run 701466  Find markers  (Find markers #14 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/701466/"

## Running Find markers [701466] [Find markers #14 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [701466] [Find markers #14 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_701466 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/701466 --iAnnot /col_attrs/Clustering_Leiden_resolution_0.8__1_ --id 469571 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/701466/exec.out 2> /data/asap2/users/1/qxj5ei/markers/701466/exec.err'"


## ----------------------------------------------------------------
## Run 723392  Find markers  (Find markers #15 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/723392/"

## Running Find markers [723392] [Find markers #15 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [723392] [Find markers #15 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_723392 --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/qxj5ei/parsing/output.loom -o /data/asap2/users/1/qxj5ei/markers/723392 --iAnnot /col_attrs/Clustering_Annotation --id 469584 --is_count_table true  1> /data/asap2/users/1/qxj5ei/markers/723392/exec.out 2> /data/asap2/users/1/qxj5ei/markers/723392/exec.err'"