## This script contains all commands executed in the PROJECT afe5sx and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT afe5sx / ASAP-21**********************'
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/afe5sx
## 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/gene_filtering/ && mkdir -p $PROJECT_DIR/normalization/ && mkdir -p $PROJECT_DIR/scaling/ && mkdir -p $PROJECT_DIR/parsing/ && mkdir -p $PROJECT_DIR/dim_reduction/ && mkdir -p $PROJECT_DIR/clustering/ && mkdir -p $PROJECT_DIR/de/ && mkdir -p $PROJECT_DIR/ge/ && mkdir -p $PROJECT_DIR/cell_filtering/"

## 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/afe5sx/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 53874  Cell filtering  (Cell filtering #1 qc_plots)
## ----------------------------------------------------------------

## 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/cell_filtering/53874/"

## writing file $PROJECT_DIR/cell_filtering/53874/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/53874/discarded_cols.json'
## writing file $PROJECT_DIR/cell_filtering/53874/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/53874/manually_discarded_cols.json'
## Running Cell filtering [53874] [Cell filtering #1 qc_plots] (Depth:4744 Detected genes:1370 Mito content:0 Protein coding content:80 Ribo content:0 Nber manually discarded cols:0 input_matrix:parsing)
echo '-> Running Cell filtering [53874] [Cell filtering #1 qc_plots] (Depth:4744 Detected genes:1370 Mito content:0 Protein coding content:80 Ribo content:0 Nber manually discarded cols:0 input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_53874 --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 FilterCols -loom /data/asap2/users/454/afe5sh/parsing/output.loom -o /data/asap2/users/454/afe5sh/cell_filtering/53858 -col_indexes_file /data/asap2/users/454/afe5sh/cell_filtering/53874/discarded_cols.json  1> /data/asap2/users/454/afe5sh/cell_filtering/53874/exec.out 2> /data/asap2/users/454/afe5sh/cell_filtering/53874/exec.err'"


## ----------------------------------------------------------------
## Run 53875  Gene filtering  (Gene filtering #1 basic)
## ----------------------------------------------------------------

## 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/gene_filtering/53875/"

## Running Gene filtering [53875] [Gene filtering #1 basic] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [53875] [Gene filtering #1 basic] (input_matrix:cell_filtering #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_53875 --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 FilterRows -loom /data/asap2/users/454/afe5sh/cell_filtering/53874/output.loom -o /data/asap2/users/454/afe5sh/gene_filtering/53859 -m basic  1> /data/asap2/users/454/afe5sh/gene_filtering/53875/exec.out 2> /data/asap2/users/454/afe5sh/gene_filtering/53875/exec.err'"


## ----------------------------------------------------------------
## Run 53876  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/53876/"

## Running Normalization [53876] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1)
echo '-> Running Normalization [53876] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_53876 --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/454/afe5sh/gene_filtering/53875/output.loom -o /data/asap2/users/454/afe5sh/normalization/53876/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/454/afe5sh/normalization/53876/exec.out 2> /data/asap2/users/454/afe5sh/normalization/53876/exec.err'"


## ----------------------------------------------------------------
## Run 53877  Scaling  (Scaling #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/scaling/53877/"

## Running Scaling [53877] [Scaling #1 asap_seurat] (input_matrix:normalization #1)
echo '-> Running Scaling [53877] [Scaling #1 asap_seurat] (input_matrix:normalization #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_53877 --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 Scaling -loom /data/asap2/users/454/afe5sh/gene_filtering/53875/output.loom -o /data/asap2/users/454/afe5sh/scaling/53877/output.json -iAnnot /layers/norm_1_asap_seurat -oAnnot /layers/scaling_1_asap_seurat -scale true -center true -scaleMax 10  1> /data/asap2/users/454/afe5sh/scaling/53877/exec.out 2> /data/asap2/users/454/afe5sh/scaling/53877/exec.err'"


## ----------------------------------------------------------------
## Run 53878  Clustering  (Clustering #1 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/clustering/53878/"

## Running Clustering [53878] [Clustering #1 seurat] (input_matrix:scaling #1)
echo '-> Running Clustering [53878] [Clustering #1 seurat] (input_matrix:scaling #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_53878 --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 clustering.R  /data/asap2/users/454/afe5sh/gene_filtering/53875/output.loom /data/asap2/users/454/afe5sh/clustering/53864 seurat /layers/scaling_1_asap_seurat /col_attrs/_clust_1_seurat 20 0.8 louvain snn 1> /data/asap2/users/454/afe5sh/clustering/53878/exec.out 2> /data/asap2/users/454/afe5sh/clustering/53878/exec.err'"


## ----------------------------------------------------------------
## Run 53879  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/53879/"

## Running Dimension reduction [53879] [Dimension reduction #1 umap] (input_matrix:scaling #1 Number of dimensions:2)
echo '-> Running Dimension reduction [53879] [Dimension reduction #1 umap] (input_matrix:scaling #1 Number of dimensions:2)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_53879 --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/454/afe5sh/gene_filtering/53875/output.loom /data/asap2/users/454/afe5sh/dim_reduction/53866 umap /layers/scaling_1_asap_seurat /col_attrs/_dr_1_umap_2D 2 0.1 30 correlation 1> /data/asap2/users/454/afe5sh/dim_reduction/53879/exec.out 2> /data/asap2/users/454/afe5sh/dim_reduction/53879/exec.err'"


## ----------------------------------------------------------------
## Run 53880  Clustering  (Clustering #2 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/clustering/53880/"

## Running Clustering [53880] [Clustering #2 seurat] (input_matrix:scaling #1 Resolution:1)
echo '-> Running Clustering [53880] [Clustering #2 seurat] (input_matrix:scaling #1 Resolution:1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_53880 --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 clustering.R  /data/asap2/users/454/afe5sh/gene_filtering/53875/output.loom /data/asap2/users/454/afe5sh/clustering/53868 seurat /layers/scaling_1_asap_seurat /col_attrs/_clust_2_seurat 20 1 louvain snn 1> /data/asap2/users/454/afe5sh/clustering/53880/exec.out 2> /data/asap2/users/454/afe5sh/clustering/53880/exec.err'"


## ----------------------------------------------------------------
## Run 53881  Clustering  (Clustering #3 kmeans)
## ----------------------------------------------------------------

## 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/clustering/53881/"

## Running Clustering [53881] [Clustering #3 kmeans] (input_matrix:scaling #1)
echo '-> Running Clustering [53881] [Clustering #3 kmeans] (input_matrix:scaling #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_53881 --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 clustering.R  /data/asap2/users/454/afe5sh/gene_filtering/53875/output.loom /data/asap2/users/454/afe5sh/clustering/53869 kmeans /layers/scaling_1_asap_seurat /col_attrs/_clust_3_kmeans 2:10 Hartigan-Wong 1> /data/asap2/users/454/afe5sh/clustering/53881/exec.out 2> /data/asap2/users/454/afe5sh/clustering/53881/exec.err'"


## ----------------------------------------------------------------
## Run 53882  Differential expression  (Differential expression #1 wilcox_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/de/53882/"

## Running Differential expression [53882] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #3 Reference group:1 Compared group:2)
echo '-> Running Differential expression [53882] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #3 Reference group:1 Compared group:2)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_53882 --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 de.R  /data/asap2/users/454/afe5sh/gene_filtering/53875/output.loom /data/asap2/users/454/afe5sh/de/53870 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_1_wilcox_seurat null /col_attrs/_clust_3_kmeans 1 2 false 0.1 null 1.3 null 16 1> /data/asap2/users/454/afe5sh/de/53882/exec.out 2> /data/asap2/users/454/afe5sh/de/53882/exec.err'"


## ----------------------------------------------------------------
## Run 53883  Differential expression  (Differential expression #2 wilcox_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/de/53883/"

## Running Differential expression [53883] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #3 Reference group:1 Compared group:2 Min % cells with gene>0:0.25 Fold change cutoff:0.2)
echo '-> Running Differential expression [53883] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #3 Reference group:1 Compared group:2 Min % cells with gene>0:0.25 Fold change cutoff:0.2)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_53883 --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 de.R  /data/asap2/users/454/afe5sh/gene_filtering/53875/output.loom /data/asap2/users/454/afe5sh/de/53871 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_2_wilcox_seurat null /col_attrs/_clust_3_kmeans 1 2 false 0.25 null 0.2 null 16 1> /data/asap2/users/454/afe5sh/de/53883/exec.out 2> /data/asap2/users/454/afe5sh/de/53883/exec.err'"


## ----------------------------------------------------------------
## Run 53884  Gene Enrichment  (Gene Enrichment #1 basic)
## ----------------------------------------------------------------

## 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/ge/53884/"

## Running Gene Enrichment [53884] [Gene Enrichment #1 basic] (input_de:de #2 Cutoff FC:1)
echo '-> Running Gene Enrichment [53884] [Gene Enrichment #1 basic] (input_de:de #2 Cutoff FC:1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_53884 --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 Enrichment -loom /data/asap2/users/454/afe5sh/gene_filtering/53875/output.loom -m fet -f /data/asap2/users/454/afe5sh/tmp/454_53871_filtered.json -o /data/asap2/users/454/afe5sh/ge/53884/output.json -max 500 -min 15 -adj fdr -geneset 52 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/454/afe5sh/ge/53884/exec.out 2> /data/asap2/users/454/afe5sh/ge/53884/exec.err'"