## This script contains all commands executed in the PROJECT 492iyz and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT 492iyz / ASAP60**********************'
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/492iyz
## 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/dim_reduction/ && 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/492iyz/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 75722  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/75722/"

## Running Normalization [75722] [Normalization #1 asap_seurat] (input_matrix:parsing)
echo '-> Running Normalization [75722] [Normalization #1 asap_seurat] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_75722 --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/1/492iyz/parsing/output.loom -o /data/asap2/users/1/492iyz/normalization/75722/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/492iyz/normalization/75722/exec.out 2> /data/asap2/users/1/492iyz/normalization/75722/exec.err'"


## ----------------------------------------------------------------
## Run 78906  Dimension reduction  (Dimension reduction #1 umap)
## ----------------------------------------------------------------

## 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/dim_reduction/78906/"

## Running Dimension reduction [78906] [Dimension reduction #1 umap] (input_matrix:normalization #1 nber_dims:2)
echo '-> Running Dimension reduction [78906] [Dimension reduction #1 umap] (input_matrix:normalization #1 nber_dims:2)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_78906 --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 dimension_reduction.R  /data/asap2/users/1/492iyz/parsing/output.loom /data/asap2/users/1/492iyz/dim_reduction/78906 umap /layers/norm_1_asap_seurat /col_attrs/_dr_1_umap_2D 2 0.1 30 correlation 1> /data/asap2/users/1/492iyz/dim_reduction/78906/exec.out 2> /data/asap2/users/1/492iyz/dim_reduction/78906/exec.err'"


## ----------------------------------------------------------------
## Run 78907  Dimension reduction  (Dimension reduction #2 umap)
## ----------------------------------------------------------------

## 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/dim_reduction/78907/"

## Running Dimension reduction [78907] [Dimension reduction #2 umap] (input_matrix:normalization #1 nber_dims:3)
echo '-> Running Dimension reduction [78907] [Dimension reduction #2 umap] (input_matrix:normalization #1 nber_dims:3)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_78907 --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 dimension_reduction.R  /data/asap2/users/1/492iyz/parsing/output.loom /data/asap2/users/1/492iyz/dim_reduction/78907 umap /layers/norm_1_asap_seurat /col_attrs/_dr_2_umap_3D 3 0.1 30 correlation 1> /data/asap2/users/1/492iyz/dim_reduction/78907/exec.out 2> /data/asap2/users/1/492iyz/dim_reduction/78907/exec.err'"


## ----------------------------------------------------------------
## Run 179563  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/179563/"

## Running Find markers [179563] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [179563] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_179563 --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/1/492iyz/parsing/output.loom -o /data/asap2/users/1/492iyz/markers/179563 --iAnnot /col_attrs/transf_annotation --id 480173  1> /data/asap2/users/1/492iyz/markers/179563/exec.out 2> /data/asap2/users/1/492iyz/markers/179563/exec.err'"


## ----------------------------------------------------------------
## Run 179564  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/179564/"

## Running Marker enrichment [179564] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [179564] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_179564 --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/1/492iyz/markers/179563 -o /data/asap2/users/1/492iyz/markers/179564 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/492iyz/markers/179564/exec.out 2> /data/asap2/users/1/492iyz/markers/179564/exec.err'"


## ----------------------------------------------------------------
## Run 583563  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/583563/"

## Running Find markers [583563] [Find markers #2 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [583563] [Find markers #2 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_583563 --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/1/492iyz/parsing/output.loom -o /data/asap2/users/1/492iyz/markers/583563 --iAnnot /col_attrs/transf_annotation --id 480173 --is_count_table true  1> /data/asap2/users/1/492iyz/markers/583563/exec.out 2> /data/asap2/users/1/492iyz/markers/583563/exec.err'"