## This script contains all commands executed in the PROJECT zs5t0p and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT zs5t0p / ASAP96**********************'
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/zs5t0p
## Pull Docker images (must run before any docker run in this script)

docker pull fabdavid/asap_run:v6

## Host LOOM staging directory (inside Docker volume)
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -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_v6; then echo 'Create database asap_data_v6'; echo '$PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v6'; $PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v6; echo 'wget -qO - https://asap.epfl.ch/dumps/asap_data_v6.sql.gz | gunzip | grep -v \'AS integer\' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v6'; wget -qO - https://asap.epfl.ch/dumps/asap_data_v6.sql.gz | gunzip | grep -v 'AS integer' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v6; fi

## Project directory on the shared volume
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR"

## 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:v6 -c "wget -qO $PROJECT_DIR/parsing/output.loom 'https://asap.epfl.ch/projects/zs5t0p/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 681216    (NA)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/parsing/"

## Running  [681216] [NA] ()
echo '-> Running  [681216] [NA] ()'

## Command
sh -c 'cd /app && RAILS_ENV=production bundle exec rails parse[zs5t0p]  '


## ----------------------------------------------------------------
## Run 688907    (NA)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/markers/688907/"

## Running  [688907] [NA] (input_matrix:NA)
echo '-> Running  [688907] [NA] (input_matrix:NA)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl -v /srv/asap_run_new/python/doublet.calling.v8.py:/srv/doublet.calling.v8.py:ro -v /srv/asap_run_new/python/doublet.scoring.v8.py:/srv/doublet.scoring.v8.py:ro -v /srv/asap_run_new/R/doublet.scoring.v8.R:/srv/doublet.scoring.v8.R:ro --name asap_dev_688907 --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:v8 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/2/zs5t0p/parsing/output.loom -o /data/asap2/users/2/zs5t0p/markers/688907 --iAnnot /col_attrs/TF --id 5114243 --is_count_table true  1> /data/asap2/users/2/zs5t0p/markers/688907/exec.out 2> /data/asap2/users/2/zs5t0p/markers/688907/exec.err'"


## ----------------------------------------------------------------
## Run 688908    (NA)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/markers/688908/"

## Running  [688908] [NA] (input_matrix:NA)
echo '-> Running  [688908] [NA] (input_matrix:NA)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl -v /srv/asap_run_new/python/doublet.calling.v8.py:/srv/doublet.calling.v8.py:ro -v /srv/asap_run_new/python/doublet.scoring.v8.py:/srv/doublet.scoring.v8.py:ro -v /srv/asap_run_new/R/doublet.scoring.v8.R:/srv/doublet.scoring.v8.R:ro --name asap_dev_688908 --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:v8 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/2/zs5t0p/parsing/output.loom -o /data/asap2/users/2/zs5t0p/markers/688908 --iAnnot /col_attrs/Phase --id 5114240 --is_count_table true  1> /data/asap2/users/2/zs5t0p/markers/688908/exec.out 2> /data/asap2/users/2/zs5t0p/markers/688908/exec.err'"


## ----------------------------------------------------------------
## Run 688909    (NA)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/markers/688909/"

## Running  [688909] [NA] (input_matrix:NA)
echo '-> Running  [688909] [NA] (input_matrix:NA)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl -v /srv/asap_run_new/python/doublet.calling.v8.py:/srv/doublet.calling.v8.py:ro -v /srv/asap_run_new/python/doublet.scoring.v8.py:/srv/doublet.scoring.v8.py:ro -v /srv/asap_run_new/R/doublet.scoring.v8.R:/srv/doublet.scoring.v8.R:ro --name asap_dev_688909 --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:v8 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/2/zs5t0p/parsing/output.loom -o /data/asap2/users/2/zs5t0p/markers/688909 --iAnnot /col_attrs/Phase_corrected --id 5114241 --is_count_table true  1> /data/asap2/users/2/zs5t0p/markers/688909/exec.out 2> /data/asap2/users/2/zs5t0p/markers/688909/exec.err'"


## ----------------------------------------------------------------
## Run 688910    (NA)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/markers/688910/"

## Running  [688910] [NA] (input_matrix:NA)
echo '-> Running  [688910] [NA] (input_matrix:NA)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl -v /srv/asap_run_new/python/doublet.calling.v8.py:/srv/doublet.calling.v8.py:ro -v /srv/asap_run_new/python/doublet.scoring.v8.py:/srv/doublet.scoring.v8.py:ro -v /srv/asap_run_new/R/doublet.scoring.v8.R:/srv/doublet.scoring.v8.R:ro --name asap_dev_688910 --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:v8 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/2/zs5t0p/parsing/output.loom -o /data/asap2/users/2/zs5t0p/markers/688910 --iAnnot /col_attrs/batch --id 5114247 --is_count_table true  1> /data/asap2/users/2/zs5t0p/markers/688910/exec.out 2> /data/asap2/users/2/zs5t0p/markers/688910/exec.err'"


## ----------------------------------------------------------------
## Run 688911    (NA)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/markers/688911/"

## Running  [688911] [NA] (input_matrix:NA)
echo '-> Running  [688911] [NA] (input_matrix:NA)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl -v /srv/asap_run_new/python/doublet.calling.v8.py:/srv/doublet.calling.v8.py:ro -v /srv/asap_run_new/python/doublet.scoring.v8.py:/srv/doublet.scoring.v8.py:ro -v /srv/asap_run_new/R/doublet.scoring.v8.R:/srv/doublet.scoring.v8.R:ro --name asap_dev_688911 --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:v8 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/2/zs5t0p/parsing/output.loom -o /data/asap2/users/2/zs5t0p/markers/688911 --iAnnot /col_attrs/functional_cells --id 5114248 --is_count_table true  1> /data/asap2/users/2/zs5t0p/markers/688911/exec.out 2> /data/asap2/users/2/zs5t0p/markers/688911/exec.err'"


## ----------------------------------------------------------------
## Run 688912    (NA)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/markers/688912/"

## Running  [688912] [NA] (input_matrix:NA)
echo '-> Running  [688912] [NA] (input_matrix:NA)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl -v /srv/asap_run_new/python/doublet.calling.v8.py:/srv/doublet.calling.v8.py:ro -v /srv/asap_run_new/python/doublet.scoring.v8.py:/srv/doublet.scoring.v8.py:ro -v /srv/asap_run_new/R/doublet.scoring.v8.R:/srv/doublet.scoring.v8.R:ro --name asap_dev_688912 --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:v8 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/2/zs5t0p/parsing/output.loom -o /data/asap2/users/2/zs5t0p/markers/688912 --iAnnot /col_attrs/orig.ident --id 5114251 --is_count_table true  1> /data/asap2/users/2/zs5t0p/markers/688912/exec.out 2> /data/asap2/users/2/zs5t0p/markers/688912/exec.err'"