## This script contains all commands executed in the PROJECT 0t47gk and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT 0t47gk / ASAP24**********************'
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/0t47gk
## 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/0t47gk/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 73700  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/73700/"

## Running Normalization [73700] [Normalization #1 asap_seurat] (input_matrix:parsing)
echo '-> Running Normalization [73700] [Normalization #1 asap_seurat] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_73700 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/normalization/73700/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/0t47gk/normalization/73700/exec.out 2> /data/asap2/users/1/0t47gk/normalization/73700/exec.err'"


## ----------------------------------------------------------------
## Run 160250  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/160250/"

## Running Find markers [160250] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [160250] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_160250 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/160250 --iAnnot /col_attrs/annotation --id 471321  1> /data/asap2/users/1/0t47gk/markers/160250/exec.out 2> /data/asap2/users/1/0t47gk/markers/160250/exec.err'"


## ----------------------------------------------------------------
## Run 160251  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/160251/"

## Running Marker enrichment [160251] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [160251] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_160251 --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/1/0t47gk/markers/160250 -o /data/asap2/users/1/0t47gk/markers/160251 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/0t47gk/markers/160251/exec.out 2> /data/asap2/users/1/0t47gk/markers/160251/exec.err'"


## ----------------------------------------------------------------
## Run 160252  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/160252/"

## Running Find markers [160252] [Find markers #2 asap_markers] ()
echo '-> Running Find markers [160252] [Find markers #2 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_160252 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/160252 --iAnnot /col_attrs/Clustering_Annotation --id 471310  1> /data/asap2/users/1/0t47gk/markers/160252/exec.out 2> /data/asap2/users/1/0t47gk/markers/160252/exec.err'"


## ----------------------------------------------------------------
## Run 160253  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/160253/"

## Running Marker enrichment [160253] [Marker enrichment #3 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [160253] [Marker enrichment #3 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_160253 --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/1/0t47gk/markers/160252 -o /data/asap2/users/1/0t47gk/markers/160253 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/0t47gk/markers/160253/exec.out 2> /data/asap2/users/1/0t47gk/markers/160253/exec.err'"


## ----------------------------------------------------------------
## Run 163374  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/163374/"

## Running Find markers [163374] [Find markers #3 asap_markers] ()
echo '-> Running Find markers [163374] [Find markers #3 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_163374 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/163374 --iAnnot /col_attrs/tissue --id 471316  1> /data/asap2/users/1/0t47gk/markers/163374/exec.out 2> /data/asap2/users/1/0t47gk/markers/163374/exec.err'"


## ----------------------------------------------------------------
## Run 163375  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/163375/"

## Running Marker enrichment [163375] [Marker enrichment #4 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [163375] [Marker enrichment #4 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_163375 --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/1/0t47gk/markers/163374 -o /data/asap2/users/1/0t47gk/markers/163375 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/0t47gk/markers/163375/exec.out 2> /data/asap2/users/1/0t47gk/markers/163375/exec.err'"


## ----------------------------------------------------------------
## Run 163376  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/163376/"

## Running Find markers [163376] [Find markers #4 asap_markers] ()
echo '-> Running Find markers [163376] [Find markers #4 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_163376 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/163376 --iAnnot /col_attrs/ClusterID --id 471289  1> /data/asap2/users/1/0t47gk/markers/163376/exec.out 2> /data/asap2/users/1/0t47gk/markers/163376/exec.err'"


## ----------------------------------------------------------------
## Run 163377  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/163377/"

## Running Marker enrichment [163377] [Marker enrichment #5 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [163377] [Marker enrichment #5 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_163377 --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/1/0t47gk/markers/163376 -o /data/asap2/users/1/0t47gk/markers/163377 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/0t47gk/markers/163377/exec.out 2> /data/asap2/users/1/0t47gk/markers/163377/exec.err'"


## ----------------------------------------------------------------
## Run 296422  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/296422/"

## Running Find markers [296422] [Find markers #5 asap_markers] ()
echo '-> Running Find markers [296422] [Find markers #5 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_296422 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/296422 --iAnnot /col_attrs/age --id 471294 --is_count_table  1> /data/asap2/users/1/0t47gk/markers/296422/exec.out 2> /data/asap2/users/1/0t47gk/markers/296422/exec.err'"


## ----------------------------------------------------------------
## Run 296423  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/296423/"

## Running Marker enrichment [296423] [Marker enrichment #6 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [296423] [Marker enrichment #6 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_296423 --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/1/0t47gk/markers/296422 -o /data/asap2/users/1/0t47gk/markers/296423 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/0t47gk/markers/296423/exec.out 2> /data/asap2/users/1/0t47gk/markers/296423/exec.err'"


## ----------------------------------------------------------------
## Run 299537  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/299537/"

## Running Find markers [299537] [Find markers #6 asap_markers] ()
echo '-> Running Find markers [299537] [Find markers #6 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_299537 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/299537 --iAnnot /col_attrs/annotation__ontology_id --id 471286 --is_count_table  1> /data/asap2/users/1/0t47gk/markers/299537/exec.out 2> /data/asap2/users/1/0t47gk/markers/299537/exec.err'"


## ----------------------------------------------------------------
## Run 299538  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/299538/"

## Running Marker enrichment [299538] [Marker enrichment #7 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [299538] [Marker enrichment #7 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_299538 --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/1/0t47gk/markers/299537 -o /data/asap2/users/1/0t47gk/markers/299538 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/0t47gk/markers/299538/exec.out 2> /data/asap2/users/1/0t47gk/markers/299538/exec.err'"


## ----------------------------------------------------------------
## Run 321557  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/321557/"

## Running Find markers [321557] [Find markers #7 asap_markers] ()
echo '-> Running Find markers [321557] [Find markers #7 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_321557 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/321557 --iAnnot /col_attrs/fly_genetics --id 471302 --is_count_table  1> /data/asap2/users/1/0t47gk/markers/321557/exec.out 2> /data/asap2/users/1/0t47gk/markers/321557/exec.err'"


## ----------------------------------------------------------------
## Run 321558  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/321558/"

## Running Marker enrichment [321558] [Marker enrichment #8 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [321558] [Marker enrichment #8 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_321558 --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/1/0t47gk/markers/321557 -o /data/asap2/users/1/0t47gk/markers/321558 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/0t47gk/markers/321558/exec.out 2> /data/asap2/users/1/0t47gk/markers/321558/exec.err'"


## ----------------------------------------------------------------
## Run 350677  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/350677/"

## Running Find markers [350677] [Find markers #8 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [350677] [Find markers #8 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_350677 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/350677 --iAnnot /col_attrs/annotation --id 471321 --is_count_table true  1> /data/asap2/users/1/0t47gk/markers/350677/exec.out 2> /data/asap2/users/1/0t47gk/markers/350677/exec.err'"


## ----------------------------------------------------------------
## Run 350678  Marker enrichment  (Marker enrichment #9 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/350678/"

## Running Marker enrichment [350678] [Marker enrichment #9 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [350678] [Marker enrichment #9 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_350678 --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/1/0t47gk/markers/350677 -o /data/asap2/users/1/0t47gk/markers/350678 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/0t47gk/markers/350678/exec.out 2> /data/asap2/users/1/0t47gk/markers/350678/exec.err'"


## ----------------------------------------------------------------
## Run 364172  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/364172/"

## Running Find markers [364172] [Find markers #9 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [364172] [Find markers #9 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_364172 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/364172 --iAnnot /col_attrs/ClusterID --id 471289 --is_count_table true  1> /data/asap2/users/1/0t47gk/markers/364172/exec.out 2> /data/asap2/users/1/0t47gk/markers/364172/exec.err'"


## ----------------------------------------------------------------
## Run 364173  Marker enrichment  (Marker enrichment #10 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/364173/"

## Running Marker enrichment [364173] [Marker enrichment #10 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [364173] [Marker enrichment #10 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_364173 --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/1/0t47gk/markers/364172 -o /data/asap2/users/1/0t47gk/markers/364173 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/0t47gk/markers/364173/exec.out 2> /data/asap2/users/1/0t47gk/markers/364173/exec.err'"


## ----------------------------------------------------------------
## Run 439283  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/439283/"

## Running Find markers [439283] [Find markers #10 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [439283] [Find markers #10 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_439283 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/439283 --iAnnot /col_attrs/S_annotation_broad --id 471296 --is_count_table true  1> /data/asap2/users/1/0t47gk/markers/439283/exec.out 2> /data/asap2/users/1/0t47gk/markers/439283/exec.err'"


## ----------------------------------------------------------------
## Run 453854  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/453854/"

## Running Find markers [453854] [Find markers #11 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [453854] [Find markers #11 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_453854 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/453854 --iAnnot /col_attrs/tissue --id 471316 --is_count_table true  1> /data/asap2/users/1/0t47gk/markers/453854/exec.out 2> /data/asap2/users/1/0t47gk/markers/453854/exec.err'"


## ----------------------------------------------------------------
## Run 453921  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/453921/"

## Running Find markers [453921] [Find markers #12 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [453921] [Find markers #12 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_453921 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/453921 --iAnnot /col_attrs/sex --id 471335 --is_count_table true  1> /data/asap2/users/1/0t47gk/markers/453921/exec.out 2> /data/asap2/users/1/0t47gk/markers/453921/exec.err'"


## ----------------------------------------------------------------
## Run 757890  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/757890/"

## Running Find markers [757890] [Find markers #13 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [757890] [Find markers #13 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_757890 --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/1/0t47gk/parsing/output.loom -o /data/asap2/users/1/0t47gk/markers/757890 --iAnnot /col_attrs/annotation__ontology_id --id 471286 --is_count_table true  1> /data/asap2/users/1/0t47gk/markers/757890/exec.out 2> /data/asap2/users/1/0t47gk/markers/757890/exec.err'"