## This script contains all commands executed in the PROJECT dprlat and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT dprlat / ASAP10**********************'
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/dprlat
## 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/normalization/ && mkdir -p $PROJECT_DIR/scaling/ && mkdir -p $PROJECT_DIR/cell_filtering/ && mkdir -p $PROJECT_DIR/gene_filtering/ && mkdir -p $PROJECT_DIR/removing_covariates/ && mkdir -p $PROJECT_DIR/de/ && mkdir -p $PROJECT_DIR/clustering/ && mkdir -p $PROJECT_DIR/ge/ && mkdir -p $PROJECT_DIR/parsing/ && mkdir -p $PROJECT_DIR/dim_reduction/ && mkdir -p $PROJECT_DIR/cell_selection/ && mkdir -p $PROJECT_DIR/markers/"

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

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


## ----------------------------------------------------------------
## Run 24764  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/24764/"

## writing file $PROJECT_DIR/cell_filtering/24764/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/24764/discarded_cols.json'
## writing file $PROJECT_DIR/cell_filtering/24764/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/24764/manually_discarded_cols.json'
## Running Cell filtering [24764] [Cell filtering #1 qc_plots] (Depth:100 Detected genes:100 Protein coding content:80 Mito content:40 Ribo content:40 Nber manually discarded cols:0 input_matrix:parsing)
echo '-> Running Cell filtering [24764] [Cell filtering #1 qc_plots] (Depth:100 Detected genes:100 Protein coding content:80 Mito content:40 Ribo content:40 Nber manually discarded cols:0 input_matrix:parsing)'

## 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 --name asap_dev_24764 --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/1/dprlat/parsing/output.loom -o /data/asap2/users/1/dprlat/cell_filtering/24764 -col_indexes_file /data/asap2/users/1/dprlat/cell_filtering/24764/discarded_cols.json  1> /data/asap2/users/1/dprlat/cell_filtering/24764/exec.out 2> /data/asap2/users/1/dprlat/cell_filtering/24764/exec.err'"


## ----------------------------------------------------------------
## Run 24770  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/24770/"

## Running Gene filtering [24770] [Gene filtering #1 basic] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [24770] [Gene filtering #1 basic] (input_matrix:cell_filtering #1)'

## 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 --name asap_dev_24770 --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/1/dprlat/cell_filtering/24764/output.loom -o /data/asap2/users/1/dprlat/gene_filtering/24770 -m basic  1> /data/asap2/users/1/dprlat/gene_filtering/24770/exec.out 2> /data/asap2/users/1/dprlat/gene_filtering/24770/exec.err'"


## ----------------------------------------------------------------
## Run 24771  Gene filtering  (Gene filtering #2 hvg_scanpy)
## ----------------------------------------------------------------

## 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/24771/"

## Running Gene filtering [24771] [Gene filtering #2 hvg_scanpy] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [24771] [Gene filtering #2 hvg_scanpy] (input_matrix:cell_filtering #1)'

## 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 --name asap_dev_24771 --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 'python3 hvg_scanpy_opti.py  /data/asap2/users/1/dprlat/cell_filtering/24764/output.loom /matrix /data/asap2/users/1/dprlat/gene_filtering/24771 0.5 0.0125 3 Inf 20 None false 1> /data/asap2/users/1/dprlat/gene_filtering/24771/exec.out 2> /data/asap2/users/1/dprlat/gene_filtering/24771/exec.err'"


## ----------------------------------------------------------------
## Run 24772  Gene filtering  (Gene filtering #3 hvg)
## ----------------------------------------------------------------

## 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/24772/"

## Running Gene filtering [24772] [Gene filtering #3 hvg] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [24772] [Gene filtering #3 hvg] (input_matrix:cell_filtering #1)'

## 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 --name asap_dev_24772 --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 filtering.R  /data/asap2/users/1/dprlat/cell_filtering/24764/output.loom /data/asap2/users/1/dprlat/gene_filtering/24772 hvg false 0.1 0.5 1> /data/asap2/users/1/dprlat/gene_filtering/24772/exec.out 2> /data/asap2/users/1/dprlat/gene_filtering/24772/exec.err'"


## ----------------------------------------------------------------
## Run 24773  Gene filtering  (Gene filtering #4 m3drop)
## ----------------------------------------------------------------

## 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/24773/"

## Running Gene filtering [24773] [Gene filtering #4 m3drop] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [24773] [Gene filtering #4 m3drop] (input_matrix:cell_filtering #1)'

## 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 --name asap_dev_24773 --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 filtering.R  /data/asap2/users/1/dprlat/cell_filtering/24764/output.loom /data/asap2/users/1/dprlat/gene_filtering/24773 m3drop 0.05 1> /data/asap2/users/1/dprlat/gene_filtering/24773/exec.out 2> /data/asap2/users/1/dprlat/gene_filtering/24773/exec.err'"


## ----------------------------------------------------------------
## Run 24774  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/24774/"

## Running Normalization [24774] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #2)
echo '-> Running Normalization [24774] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #2)'

## 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 --name asap_dev_24774 --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/dprlat/gene_filtering/24771/output.loom -o /data/asap2/users/1/dprlat/normalization/24774/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/dprlat/normalization/24774/exec.out 2> /data/asap2/users/1/dprlat/normalization/24774/exec.err'"


## ----------------------------------------------------------------
## Run 24775  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/24775/"

## Running Scaling [24775] [Scaling #1 asap_seurat] (input_matrix:normalization #1)
echo '-> Running Scaling [24775] [Scaling #1 asap_seurat] (input_matrix:normalization #1)'

## 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 --name asap_dev_24775 --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/1/dprlat/gene_filtering/24771/output.loom -o /data/asap2/users/1/dprlat/scaling/24775/output.json -iAnnot /layers/norm_1_asap_seurat -oAnnot /layers/scaling_1_asap_seurat -scale true -center true -scaleMax 10  1> /data/asap2/users/1/dprlat/scaling/24775/exec.out 2> /data/asap2/users/1/dprlat/scaling/24775/exec.err'"


## ----------------------------------------------------------------
## Run 24776  Dimension reduction  (Dimension reduction #1 inc_pca)
## ----------------------------------------------------------------

## 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/24776/"

## Running Dimension reduction [24776] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1)
echo '-> Running Dimension reduction [24776] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1)'

## 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 --name asap_dev_24776 --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 'python3 pca_scanpy_opti.py  /data/asap2/users/1/dprlat/gene_filtering/24771/output.loom /layers/scaling_1_asap_seurat /col_attrs/_dr_1_inc_pca_50D /data/asap2/users/1/dprlat/dim_reduction/24776/output.json 50 10000 20 1> /data/asap2/users/1/dprlat/dim_reduction/24776/exec.out 2> /data/asap2/users/1/dprlat/dim_reduction/24776/exec.err'"


## ----------------------------------------------------------------
## Run 24777  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/24777/"

## Running Dimension reduction [24777] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 Number of dimensions:2)
echo '-> Running Dimension reduction [24777] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 Number of dimensions:2)'

## 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 --name asap_dev_24777 --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/dprlat/gene_filtering/24771/output.loom /data/asap2/users/1/dprlat/dim_reduction/24777 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_2_umap_2D 2 0.1 30 correlation 1> /data/asap2/users/1/dprlat/dim_reduction/24777/exec.out 2> /data/asap2/users/1/dprlat/dim_reduction/24777/exec.err'"


## ----------------------------------------------------------------
## Run 24778  Dimension reduction  (Dimension reduction #3 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/24778/"

## Running Dimension reduction [24778] [Dimension reduction #3 umap] (input_matrix:dim_reduction #1 Number of dimensions:3)
echo '-> Running Dimension reduction [24778] [Dimension reduction #3 umap] (input_matrix:dim_reduction #1 Number of dimensions:3)'

## 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 --name asap_dev_24778 --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/dprlat/gene_filtering/24771/output.loom /data/asap2/users/1/dprlat/dim_reduction/24778 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_3_umap_3D 3 0.1 30 correlation 1> /data/asap2/users/1/dprlat/dim_reduction/24778/exec.out 2> /data/asap2/users/1/dprlat/dim_reduction/24778/exec.err'"


## ----------------------------------------------------------------
## Run 24779  Dimension reduction  (Dimension reduction #4 tsne)
## ----------------------------------------------------------------

## 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/24779/"

## Running Dimension reduction [24779] [Dimension reduction #4 tsne] (input_matrix:dim_reduction #1 Number of dimensions:2)
echo '-> Running Dimension reduction [24779] [Dimension reduction #4 tsne] (input_matrix:dim_reduction #1 Number of dimensions:2)'

## 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 --name asap_dev_24779 --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/dprlat/gene_filtering/24771/output.loom /data/asap2/users/1/dprlat/dim_reduction/24779 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_4_tsne_2D 2 30 0.5 1> /data/asap2/users/1/dprlat/dim_reduction/24779/exec.out 2> /data/asap2/users/1/dprlat/dim_reduction/24779/exec.err'"


## ----------------------------------------------------------------
## Run 24780  Dimension reduction  (Dimension reduction #5 tsne)
## ----------------------------------------------------------------

## 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/24780/"

## Running Dimension reduction [24780] [Dimension reduction #5 tsne] (input_matrix:dim_reduction #1 Number of dimensions:3)
echo '-> Running Dimension reduction [24780] [Dimension reduction #5 tsne] (input_matrix:dim_reduction #1 Number of dimensions:3)'

## 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 --name asap_dev_24780 --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/dprlat/gene_filtering/24771/output.loom /data/asap2/users/1/dprlat/dim_reduction/24780 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_5_tsne_3D 3 30 0.5 1> /data/asap2/users/1/dprlat/dim_reduction/24780/exec.out 2> /data/asap2/users/1/dprlat/dim_reduction/24780/exec.err'"


## ----------------------------------------------------------------
## Run 24781  Dimension reduction  (Dimension reduction #6 tsne_scanpy)
## ----------------------------------------------------------------

## 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/24781/"

## Running Dimension reduction [24781] [Dimension reduction #6 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:2)
echo '-> Running Dimension reduction [24781] [Dimension reduction #6 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:2)'

## 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 --name asap_dev_24781 --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 'python3 tsne_scanpy_opti.py  /data/asap2/users/1/dprlat/gene_filtering/24771/output.loom /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_6_tsne_scanpy_2D /data/asap2/users/1/dprlat/dim_reduction/24781/output.json 2 30 12 200 0 20 1> /data/asap2/users/1/dprlat/dim_reduction/24781/exec.out 2> /data/asap2/users/1/dprlat/dim_reduction/24781/exec.err'"


## ----------------------------------------------------------------
## Run 24782  Dimension reduction  (Dimension reduction #7 tsne_scanpy)
## ----------------------------------------------------------------

## 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/24782/"

## Running Dimension reduction [24782] [Dimension reduction #7 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:3)
echo '-> Running Dimension reduction [24782] [Dimension reduction #7 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:3)'

## 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 --name asap_dev_24782 --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 'python3 tsne_scanpy_opti.py  /data/asap2/users/1/dprlat/gene_filtering/24771/output.loom /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_7_tsne_scanpy_3D /data/asap2/users/1/dprlat/dim_reduction/24782/output.json 3 30 12 200 0 20 1> /data/asap2/users/1/dprlat/dim_reduction/24782/exec.out 2> /data/asap2/users/1/dprlat/dim_reduction/24782/exec.err'"


## ----------------------------------------------------------------
## Run 24783  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/24783/"

## Running Clustering [24783] [Clustering #1 seurat] (input_matrix:dim_reduction #1)
echo '-> Running Clustering [24783] [Clustering #1 seurat] (input_matrix:dim_reduction #1)'

## 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 --name asap_dev_24783 --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/1/dprlat/gene_filtering/24771/output.loom /data/asap2/users/1/dprlat/clustering/24783 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_1_seurat 20 0.8 louvain snn 1> /data/asap2/users/1/dprlat/clustering/24783/exec.out 2> /data/asap2/users/1/dprlat/clustering/24783/exec.err'"


## ----------------------------------------------------------------
## Run 24784  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/24784/"

## Running Clustering [24784] [Clustering #2 seurat] (input_matrix:dim_reduction #1 Graph type:nn)
echo '-> Running Clustering [24784] [Clustering #2 seurat] (input_matrix:dim_reduction #1 Graph type:nn)'

## 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 --name asap_dev_24784 --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/1/dprlat/gene_filtering/24771/output.loom /data/asap2/users/1/dprlat/clustering/24784 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_2_seurat 20 0.8 louvain nn 1> /data/asap2/users/1/dprlat/clustering/24784/exec.out 2> /data/asap2/users/1/dprlat/clustering/24784/exec.err'"


## ----------------------------------------------------------------
## Run 24785  Cell selection  (Cell selection #1 cell_sel)
## ----------------------------------------------------------------

## 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_selection/24785/"

## Running Cell selection [24785] [Cell selection #1 cell_sel] ()
echo '-> Running Cell selection [24785] [Cell selection #1 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/dprlat/gene_filtering/24771/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_1 -f /data/asap2/users/1/dprlat/metadata/24785/list_cols.json '


## ----------------------------------------------------------------
## Run 24786  Cell selection  (Cell selection #2 cell_sel)
## ----------------------------------------------------------------

## 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_selection/24786/"

## Running Cell selection [24786] [Cell selection #2 cell_sel] ()
echo '-> Running Cell selection [24786] [Cell selection #2 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/dprlat/gene_filtering/24771/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_2 -f /data/asap2/users/1/dprlat/metadata/24786/list_cols.json '


## ----------------------------------------------------------------
## Run 24822  Differential expression  (Differential expression #1 wilcox_asap)
## ----------------------------------------------------------------

## 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/24822/"

## Running Differential expression [24822] [Differential expression #1 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:4 Compared group:)
echo '-> Running Differential expression [24822] [Differential expression #1 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:4 Compared group:)'

## 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 --name asap_dev_24822 --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 DifferentialExpression -loom /data/asap2/users/1/dprlat/gene_filtering/24771/output.loom -o /data/asap2/users/1/dprlat/de/24822 -m wilcox_asap -iAnnot /layers/norm_1_asap_seurat -oAnnot /row_attrs/_de_1_wilcox_asap -gAnnot /col_attrs/_clust_1_seurat -g1 4 -g2 null  1> /data/asap2/users/1/dprlat/de/24822/exec.out 2> /data/asap2/users/1/dprlat/de/24822/exec.err'"


## ----------------------------------------------------------------
## Run 24824  Differential expression  (Differential expression #3 wilcox_asap)
## ----------------------------------------------------------------

## 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/24824/"

## Running Differential expression [24824] [Differential expression #3 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:10 Compared group:)
echo '-> Running Differential expression [24824] [Differential expression #3 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:10 Compared group:)'

## 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 --name asap_dev_24824 --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 DifferentialExpression -loom /data/asap2/users/1/dprlat/gene_filtering/24771/output.loom -o /data/asap2/users/1/dprlat/de/24824 -m wilcox_asap -iAnnot /layers/norm_1_asap_seurat -oAnnot /row_attrs/_de_3_wilcox_asap -gAnnot /col_attrs/_clust_1_seurat -g1 10 -g2 null  1> /data/asap2/users/1/dprlat/de/24824/exec.out 2> /data/asap2/users/1/dprlat/de/24824/exec.err'"


## ----------------------------------------------------------------
## Run 24825  Differential expression  (Differential expression #4 wilcox_asap)
## ----------------------------------------------------------------

## 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/24825/"

## Running Differential expression [24825] [Differential expression #4 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:20 Compared group:)
echo '-> Running Differential expression [24825] [Differential expression #4 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:20 Compared group:)'

## 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 --name asap_dev_24825 --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 DifferentialExpression -loom /data/asap2/users/1/dprlat/gene_filtering/24771/output.loom -o /data/asap2/users/1/dprlat/de/24825 -m wilcox_asap -iAnnot /layers/norm_1_asap_seurat -oAnnot /row_attrs/_de_4_wilcox_asap -gAnnot /col_attrs/_clust_1_seurat -g1 20 -g2 null  1> /data/asap2/users/1/dprlat/de/24825/exec.out 2> /data/asap2/users/1/dprlat/de/24825/exec.err'"


## ----------------------------------------------------------------
## Run 24826  Differential expression  (Differential expression #5 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/24826/"

## Running Differential expression [24826] [Differential expression #5 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:20 Compared group:)
echo '-> Running Differential expression [24826] [Differential expression #5 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:20 Compared group:)'

## 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 --name asap_dev_24826 --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/1/dprlat/gene_filtering/24771/output.loom /data/asap2/users/1/dprlat/de/24826 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_5_wilcox_seurat null /col_attrs/_clust_1_seurat 20 null false 0.1 null 1.3 null 1> /data/asap2/users/1/dprlat/de/24826/exec.out 2> /data/asap2/users/1/dprlat/de/24826/exec.err'"


## ----------------------------------------------------------------
## Run 24827  Differential expression  (Differential expression #6 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/24827/"

## Running Differential expression [24827] [Differential expression #6 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:10 Compared group:)
echo '-> Running Differential expression [24827] [Differential expression #6 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:10 Compared group:)'

## 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 --name asap_dev_24827 --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/1/dprlat/gene_filtering/24771/output.loom /data/asap2/users/1/dprlat/de/24827 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_6_wilcox_seurat null /col_attrs/_clust_1_seurat 10 null false 0.1 null 1.3 null 1> /data/asap2/users/1/dprlat/de/24827/exec.out 2> /data/asap2/users/1/dprlat/de/24827/exec.err'"


## ----------------------------------------------------------------
## Run 24828  Differential expression  (Differential expression #7 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/24828/"

## Running Differential expression [24828] [Differential expression #7 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:4 Compared group:)
echo '-> Running Differential expression [24828] [Differential expression #7 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:4 Compared group:)'

## 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 --name asap_dev_24828 --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/1/dprlat/gene_filtering/24771/output.loom /data/asap2/users/1/dprlat/de/24828 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_7_wilcox_seurat null /col_attrs/_clust_1_seurat 4 null false 0.1 null 1.3 null 1> /data/asap2/users/1/dprlat/de/24828/exec.out 2> /data/asap2/users/1/dprlat/de/24828/exec.err'"


## ----------------------------------------------------------------
## Run 24829  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/24829/"

## Running Gene Enrichment [24829] [Gene Enrichment #1 basic] (input_de:de #4)
echo '-> Running Gene Enrichment [24829] [Gene Enrichment #1 basic] (input_de:de #4)'

## 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 --name asap_dev_24829 --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/1/dprlat/gene_filtering/24771/output.loom -m fet -f /data/asap2/users/1/dprlat/tmp/1_24825_2_0.05_filtered_ids.json -o /data/asap2/users/1/dprlat/ge/24829/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/dprlat/ge/24829/exec.out 2> /data/asap2/users/1/dprlat/ge/24829/exec.err'"


## ----------------------------------------------------------------
## Run 24830  Gene Enrichment  (Gene Enrichment #2 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/24830/"

## Running Gene Enrichment [24830] [Gene Enrichment #2 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24830] [Gene Enrichment #2 basic] (input_de:de #3)'

## 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 --name asap_dev_24830 --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/1/dprlat/gene_filtering/24771/output.loom -m fet -f /data/asap2/users/1/dprlat/tmp/1_24824_2_0.05_filtered_ids.json -o /data/asap2/users/1/dprlat/ge/24830/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/dprlat/ge/24830/exec.out 2> /data/asap2/users/1/dprlat/ge/24830/exec.err'"


## ----------------------------------------------------------------
## Run 24831  Gene Enrichment  (Gene Enrichment #3 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/24831/"

## Running Gene Enrichment [24831] [Gene Enrichment #3 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24831] [Gene Enrichment #3 basic] (input_de:de #1)'

## 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 --name asap_dev_24831 --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/1/dprlat/gene_filtering/24771/output.loom -m fet -f /data/asap2/users/1/dprlat/tmp/1_24822_2_0.05_filtered_ids.json -o /data/asap2/users/1/dprlat/ge/24831/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/dprlat/ge/24831/exec.out 2> /data/asap2/users/1/dprlat/ge/24831/exec.err'"


## ----------------------------------------------------------------
## Run 24832  Gene Enrichment  (Gene Enrichment #4 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/24832/"

## Running Gene Enrichment [24832] [Gene Enrichment #4 basic] (input_de:de #6)
echo '-> Running Gene Enrichment [24832] [Gene Enrichment #4 basic] (input_de:de #6)'

## 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 --name asap_dev_24832 --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/1/dprlat/gene_filtering/24771/output.loom -m fet -f /data/asap2/users/1/dprlat/tmp/1_24827_2_0.05_filtered_ids.json -o /data/asap2/users/1/dprlat/ge/24832/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/dprlat/ge/24832/exec.out 2> /data/asap2/users/1/dprlat/ge/24832/exec.err'"


## ----------------------------------------------------------------
## Run 24833  Gene Enrichment  (Gene Enrichment #5 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/24833/"

## Running Gene Enrichment [24833] [Gene Enrichment #5 basic] (input_de:de #7)
echo '-> Running Gene Enrichment [24833] [Gene Enrichment #5 basic] (input_de:de #7)'

## 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 --name asap_dev_24833 --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/1/dprlat/gene_filtering/24771/output.loom -m fet -f /data/asap2/users/1/dprlat/tmp/1_24828_2_0.05_filtered_ids.json -o /data/asap2/users/1/dprlat/ge/24833/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/dprlat/ge/24833/exec.out 2> /data/asap2/users/1/dprlat/ge/24833/exec.err'"


## ----------------------------------------------------------------
## Run 24834  Gene Enrichment  (Gene Enrichment #6 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/24834/"

## Running Gene Enrichment [24834] [Gene Enrichment #6 basic] (input_de:de #5)
echo '-> Running Gene Enrichment [24834] [Gene Enrichment #6 basic] (input_de:de #5)'

## 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 --name asap_dev_24834 --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/1/dprlat/gene_filtering/24771/output.loom -m fet -f /data/asap2/users/1/dprlat/tmp/1_24826_2_0.05_filtered_ids.json -o /data/asap2/users/1/dprlat/ge/24834/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/dprlat/ge/24834/exec.out 2> /data/asap2/users/1/dprlat/ge/24834/exec.err'"


## ----------------------------------------------------------------
## Run 66107  Removing covariates  (Removing covariates #1 fastmnn)
## ----------------------------------------------------------------

## 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/removing_covariates/66107/"

## Running Removing covariates [66107] [Removing covariates #1 fastmnn] (input_matrix:normalization #1 covariates:gene_filtering #2)
echo '-> Running Removing covariates [66107] [Removing covariates #1 fastmnn] (input_matrix:normalization #1 covariates:gene_filtering #2)'

## 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 --name asap_dev_66107 --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 batch.asap.2.R  /data/asap2/users/1/dprlat/gene_filtering/24771/output.loom /data/asap2/users/1/dprlat/removing_covariates/66107 fastmnn /layers/norm_1_asap_seurat /layers/rmcov_1_fastmnn /col_attrs/donor_organism.is_living 20 3 50 1> /data/asap2/users/1/dprlat/removing_covariates/66107/exec.out 2> /data/asap2/users/1/dprlat/removing_covariates/66107/exec.err'"


## ----------------------------------------------------------------
## Run 726202  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/726202/"

## Running Find markers [726202] [Find markers #1 asap_markers] (input_matrix:gene_filtering #2)
echo '-> Running Find markers [726202] [Find markers #1 asap_markers] (input_matrix:gene_filtering #2)'

## 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 --name asap_dev_726202 --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/dprlat/gene_filtering/24771/output.loom -o /data/asap2/users/1/dprlat/markers/726202 --iAnnot /col_attrs/_clust_2_seurat --id 109388 --is_count_table true  1> /data/asap2/users/1/dprlat/markers/726202/exec.out 2> /data/asap2/users/1/dprlat/markers/726202/exec.err'"


## ----------------------------------------------------------------
## Run 750677  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/750677/"

## Running Find markers [750677] [Find markers #2 asap_markers] (input_matrix:gene_filtering #2)
echo '-> Running Find markers [750677] [Find markers #2 asap_markers] (input_matrix:gene_filtering #2)'

## 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 --name asap_dev_750677 --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/dprlat/gene_filtering/24771/output.loom -o /data/asap2/users/1/dprlat/markers/750677 --iAnnot /col_attrs/derived_organ_label --id 109172 --is_count_table true  1> /data/asap2/users/1/dprlat/markers/750677/exec.out 2> /data/asap2/users/1/dprlat/markers/750677/exec.err'"


## ----------------------------------------------------------------
## Run 750678  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/750678/"

## Running Find markers [750678] [Find markers #3 asap_markers] (input_matrix:gene_filtering #2)
echo '-> Running Find markers [750678] [Find markers #3 asap_markers] (input_matrix:gene_filtering #2)'

## 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 --name asap_dev_750678 --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/dprlat/gene_filtering/24771/output.loom -o /data/asap2/users/1/dprlat/markers/750678 --iAnnot /col_attrs/cell_suspension.provenance.document_id --id 109116 --is_count_table true  1> /data/asap2/users/1/dprlat/markers/750678/exec.out 2> /data/asap2/users/1/dprlat/markers/750678/exec.err'"