## This script contains all commands executed in the PROJECT jxqlng and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT jxqlng / ASAP59**********************'
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/jxqlng
## 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/jxqlng/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 73665  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/73665/"

## Running Normalization [73665] [Normalization #1 asap_seurat] (input_matrix:parsing scale_factor:10000)
echo '-> Running Normalization [73665] [Normalization #1 asap_seurat] (input_matrix:parsing scale_factor:10000)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_73665 --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/jxqlng/parsing/output.loom -o /data/asap2/users/1/jxqlng/normalization/73665/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/jxqlng/normalization/73665/exec.out 2> /data/asap2/users/1/jxqlng/normalization/73665/exec.err'"


## ----------------------------------------------------------------
## Run 227468  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/227468/"

## Running Find markers [227468] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [227468] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_227468 --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/jxqlng/parsing/output.loom -o /data/asap2/users/1/jxqlng/markers/227468 --iAnnot /col_attrs/annotation --id 469756 --is_count_table   1> /data/asap2/users/1/jxqlng/markers/227468/exec.out 2> /data/asap2/users/1/jxqlng/markers/227468/exec.err'"


## ----------------------------------------------------------------
## Run 227469  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/227469/"

## Running Marker enrichment [227469] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [227469] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_227469 --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/jxqlng/markers/227468 -o /data/asap2/users/1/jxqlng/markers/227469 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/jxqlng/markers/227469/exec.out 2> /data/asap2/users/1/jxqlng/markers/227469/exec.err'"


## ----------------------------------------------------------------
## Run 233469  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/233469/"

## Running Find markers [233469] [Find markers #2 asap_markers] ()
echo '-> Running Find markers [233469] [Find markers #2 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_233469 --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/jxqlng/parsing/output.loom -o /data/asap2/users/1/jxqlng/markers/233469 --iAnnot /col_attrs/Clustering_Leiden_resolution_0.6 --id 469776 --is_count_table   1> /data/asap2/users/1/jxqlng/markers/233469/exec.out 2> /data/asap2/users/1/jxqlng/markers/233469/exec.err'"


## ----------------------------------------------------------------
## Run 233470  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/233470/"

## Running Marker enrichment [233470] [Marker enrichment #3 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [233470] [Marker enrichment #3 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_233470 --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/jxqlng/markers/233469 -o /data/asap2/users/1/jxqlng/markers/233470 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/jxqlng/markers/233470/exec.out 2> /data/asap2/users/1/jxqlng/markers/233470/exec.err'"


## ----------------------------------------------------------------
## Run 233471  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/233471/"

## Running Find markers [233471] [Find markers #3 asap_markers] ()
echo '-> Running Find markers [233471] [Find markers #3 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_233471 --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/jxqlng/parsing/output.loom -o /data/asap2/users/1/jxqlng/markers/233471 --iAnnot /col_attrs/Clustering_Leiden_resolution_0.4__default__397_ --id 469774 --is_count_table   1> /data/asap2/users/1/jxqlng/markers/233471/exec.out 2> /data/asap2/users/1/jxqlng/markers/233471/exec.err'"


## ----------------------------------------------------------------
## Run 233472  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/233472/"

## Running Marker enrichment [233472] [Marker enrichment #4 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [233472] [Marker enrichment #4 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_233472 --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/jxqlng/markers/233471 -o /data/asap2/users/1/jxqlng/markers/233472 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/jxqlng/markers/233472/exec.out 2> /data/asap2/users/1/jxqlng/markers/233472/exec.err'"


## ----------------------------------------------------------------
## Run 352607  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/352607/"

## Running Find markers [352607] [Find markers #4 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [352607] [Find markers #4 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_352607 --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/jxqlng/parsing/output.loom -o /data/asap2/users/1/jxqlng/markers/352607 --iAnnot /col_attrs/annotation --id 469756 --is_count_table true  1> /data/asap2/users/1/jxqlng/markers/352607/exec.out 2> /data/asap2/users/1/jxqlng/markers/352607/exec.err'"


## ----------------------------------------------------------------
## Run 352608  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/352608/"

## Running Marker enrichment [352608] [Marker enrichment #5 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [352608] [Marker enrichment #5 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_352608 --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/jxqlng/markers/352607 -o /data/asap2/users/1/jxqlng/markers/352608 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/jxqlng/markers/352608/exec.out 2> /data/asap2/users/1/jxqlng/markers/352608/exec.err'"


## ----------------------------------------------------------------
## Run 650122  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/650122/"

## Running Find markers [650122] [Find markers #5 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [650122] [Find markers #5 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_650122 --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/jxqlng/parsing/output.loom -o /data/asap2/users/1/jxqlng/markers/650122 --iAnnot /col_attrs/sex --id 469773 --is_count_table true  1> /data/asap2/users/1/jxqlng/markers/650122/exec.out 2> /data/asap2/users/1/jxqlng/markers/650122/exec.err'"