## This script contains all commands executed in the PROJECT bjtwkg and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT bjtwkg / ASAP9**********************'
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/bjtwkg
## 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/de/ && mkdir -p $PROJECT_DIR/clustering/ && mkdir -p $PROJECT_DIR/ge/ && mkdir -p $PROJECT_DIR/marker_enrich/ && 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/bjtwkg/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 24656  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/24656/"

## Running Cell selection [24656] [Cell selection #1 cell_sel] ()
echo '-> Running Cell selection [24656] [Cell selection #1 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/bjtwkg/gene_filtering/24650/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_1 -f /data/asap2/users/1/bjtwkg/metadata/24656/list_cols.json '


## ----------------------------------------------------------------
## Run 24657  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/24657/"

## Running Cell selection [24657] [Cell selection #2 cell_sel] ()
echo '-> Running Cell selection [24657] [Cell selection #2 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/bjtwkg/gene_filtering/24650/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_2 -f /data/asap2/users/1/bjtwkg/metadata/24657/list_cols.json '


## ----------------------------------------------------------------
## Run 24658  Cell selection  (Cell selection #3 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/24658/"

## Running Cell selection [24658] [Cell selection #3 cell_sel] ()
echo '-> Running Cell selection [24658] [Cell selection #3 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/bjtwkg/gene_filtering/24650/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_3 -f /data/asap2/users/1/bjtwkg/metadata/24658/list_cols.json '


## ----------------------------------------------------------------
## Run 24659  Cell selection  (Cell selection #4 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/24659/"

## Running Cell selection [24659] [Cell selection #4 cell_sel] ()
echo '-> Running Cell selection [24659] [Cell selection #4 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/bjtwkg/gene_filtering/24650/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_4 -f /data/asap2/users/1/bjtwkg/metadata/24659/list_cols.json '


## ----------------------------------------------------------------
## Run 24660  Cell selection  (Cell selection #5 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/24660/"

## Running Cell selection [24660] [Cell selection #5 cell_sel] ()
echo '-> Running Cell selection [24660] [Cell selection #5 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/bjtwkg/gene_filtering/24650/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_5 -f /data/asap2/users/1/bjtwkg/metadata/24660/list_cols.json '


## ----------------------------------------------------------------
## Run 24666  Cell selection  (Cell selection #6 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/24666/"

## Running Cell selection [24666] [Cell selection #6 cell_sel] ()
echo '-> Running Cell selection [24666] [Cell selection #6 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/bjtwkg/gene_filtering/24650/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_6 -f /data/asap2/users/1/bjtwkg/metadata/24666/list_cols.json '


## ----------------------------------------------------------------
## Run 24695  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/24695/"

## writing file $PROJECT_DIR/cell_filtering/24695/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/24695/discarded_cols.json'
## writing file $PROJECT_DIR/cell_filtering/24695/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/24695/manually_discarded_cols.json'
## Running Cell filtering [24695] [Cell filtering #1 qc_plots] (Depth:1000 Detected genes:1000 Protein coding content:80 Mito content:20 Ribo content:20 Nber manually discarded cols:0 input_matrix:parsing)
echo '-> Running Cell filtering [24695] [Cell filtering #1 qc_plots] (Depth:1000 Detected genes:1000 Protein coding content:80 Mito content:20 Ribo content:20 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_24695 --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/bjtwkg/parsing/output.loom -o /data/asap2/users/1/bjtwkg/cell_filtering/24695 -col_indexes_file /data/asap2/users/1/bjtwkg/cell_filtering/24695/discarded_cols.json  1> /data/asap2/users/1/bjtwkg/cell_filtering/24695/exec.out 2> /data/asap2/users/1/bjtwkg/cell_filtering/24695/exec.err'"


## ----------------------------------------------------------------
## Run 24697  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/24697/"

## Running Gene filtering [24697] [Gene filtering #1 basic] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [24697] [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_24697 --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/bjtwkg/cell_filtering/24695/output.loom -o /data/asap2/users/1/bjtwkg/gene_filtering/24697 -m basic  1> /data/asap2/users/1/bjtwkg/gene_filtering/24697/exec.out 2> /data/asap2/users/1/bjtwkg/gene_filtering/24697/exec.err'"


## ----------------------------------------------------------------
## Run 24699  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/24699/"

## Running Gene filtering [24699] [Gene filtering #3 hvg] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [24699] [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_24699 --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/bjtwkg/cell_filtering/24695/output.loom /data/asap2/users/1/bjtwkg/gene_filtering/24699 hvg false 0.1 0.5 1> /data/asap2/users/1/bjtwkg/gene_filtering/24699/exec.out 2> /data/asap2/users/1/bjtwkg/gene_filtering/24699/exec.err'"


## ----------------------------------------------------------------
## Run 24700  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/24700/"

## Running Gene filtering [24700] [Gene filtering #4 m3drop] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [24700] [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_24700 --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/bjtwkg/cell_filtering/24695/output.loom /data/asap2/users/1/bjtwkg/gene_filtering/24700 m3drop 0.05 1> /data/asap2/users/1/bjtwkg/gene_filtering/24700/exec.out 2> /data/asap2/users/1/bjtwkg/gene_filtering/24700/exec.err'"


## ----------------------------------------------------------------
## Run 24701  Gene filtering  (Gene filtering #5 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/24701/"

## Running Gene filtering [24701] [Gene filtering #5 hvg_scanpy] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [24701] [Gene filtering #5 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_24701 --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/bjtwkg/cell_filtering/24695/output.loom /matrix /data/asap2/users/1/bjtwkg/gene_filtering/24701 0.5 0.0125 3 Inf 20 None false 1> /data/asap2/users/1/bjtwkg/gene_filtering/24701/exec.out 2> /data/asap2/users/1/bjtwkg/gene_filtering/24701/exec.err'"


## ----------------------------------------------------------------
## Run 24704  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/24704/"

## Running Normalization [24704] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #3)
echo '-> Running Normalization [24704] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #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_24704 --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/bjtwkg/gene_filtering/24699/output.loom -o /data/asap2/users/1/bjtwkg/normalization/24704/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/bjtwkg/normalization/24704/exec.out 2> /data/asap2/users/1/bjtwkg/normalization/24704/exec.err'"


## ----------------------------------------------------------------
## Run 24705  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/24705/"

## Running Scaling [24705] [Scaling #1 asap_seurat] (input_matrix:normalization #1)
echo '-> Running Scaling [24705] [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_24705 --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/bjtwkg/gene_filtering/24699/output.loom -o /data/asap2/users/1/bjtwkg/scaling/24705/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/bjtwkg/scaling/24705/exec.out 2> /data/asap2/users/1/bjtwkg/scaling/24705/exec.err'"


## ----------------------------------------------------------------
## Run 24706  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/24706/"

## Running Dimension reduction [24706] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1)
echo '-> Running Dimension reduction [24706] [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_24706 --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/bjtwkg/gene_filtering/24699/output.loom /layers/scaling_1_asap_seurat /col_attrs/_dr_1_inc_pca_50D /data/asap2/users/1/bjtwkg/dim_reduction/24706/output.json 50 10000 20 1> /data/asap2/users/1/bjtwkg/dim_reduction/24706/exec.out 2> /data/asap2/users/1/bjtwkg/dim_reduction/24706/exec.err'"


## ----------------------------------------------------------------
## Run 24724  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/24724/"

## Running Dimension reduction [24724] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 Number of dimensions:2)
echo '-> Running Dimension reduction [24724] [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_24724 --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/bjtwkg/gene_filtering/24699/output.loom /data/asap2/users/1/bjtwkg/dim_reduction/24724 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_2_umap_2D 2 0.1 30 correlation 1> /data/asap2/users/1/bjtwkg/dim_reduction/24724/exec.out 2> /data/asap2/users/1/bjtwkg/dim_reduction/24724/exec.err'"


## ----------------------------------------------------------------
## Run 24725  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/24725/"

## Running Dimension reduction [24725] [Dimension reduction #3 umap] (input_matrix:dim_reduction #1 Number of dimensions:3)
echo '-> Running Dimension reduction [24725] [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_24725 --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/bjtwkg/gene_filtering/24699/output.loom /data/asap2/users/1/bjtwkg/dim_reduction/24725 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_3_umap_3D 3 0.1 30 correlation 1> /data/asap2/users/1/bjtwkg/dim_reduction/24725/exec.out 2> /data/asap2/users/1/bjtwkg/dim_reduction/24725/exec.err'"


## ----------------------------------------------------------------
## Run 24726  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/24726/"

## Running Dimension reduction [24726] [Dimension reduction #4 tsne] (input_matrix:dim_reduction #1 Number of dimensions:2)
echo '-> Running Dimension reduction [24726] [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_24726 --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/bjtwkg/gene_filtering/24699/output.loom /data/asap2/users/1/bjtwkg/dim_reduction/24726 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_4_tsne_2D 2 30 0.5 1> /data/asap2/users/1/bjtwkg/dim_reduction/24726/exec.out 2> /data/asap2/users/1/bjtwkg/dim_reduction/24726/exec.err'"


## ----------------------------------------------------------------
## Run 24727  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/24727/"

## Running Dimension reduction [24727] [Dimension reduction #5 tsne] (input_matrix:dim_reduction #1 Number of dimensions:3)
echo '-> Running Dimension reduction [24727] [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_24727 --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/bjtwkg/gene_filtering/24699/output.loom /data/asap2/users/1/bjtwkg/dim_reduction/24727 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_5_tsne_3D 3 30 0.5 1> /data/asap2/users/1/bjtwkg/dim_reduction/24727/exec.out 2> /data/asap2/users/1/bjtwkg/dim_reduction/24727/exec.err'"


## ----------------------------------------------------------------
## Run 24728  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/24728/"

## Running Dimension reduction [24728] [Dimension reduction #6 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:2)
echo '-> Running Dimension reduction [24728] [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_24728 --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/bjtwkg/gene_filtering/24699/output.loom /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_6_tsne_scanpy_2D /data/asap2/users/1/bjtwkg/dim_reduction/24728/output.json 2 30 12 200 0 20 1> /data/asap2/users/1/bjtwkg/dim_reduction/24728/exec.out 2> /data/asap2/users/1/bjtwkg/dim_reduction/24728/exec.err'"


## ----------------------------------------------------------------
## Run 24729  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/24729/"

## Running Dimension reduction [24729] [Dimension reduction #7 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:3)
echo '-> Running Dimension reduction [24729] [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_24729 --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/bjtwkg/gene_filtering/24699/output.loom /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_7_tsne_scanpy_3D /data/asap2/users/1/bjtwkg/dim_reduction/24729/output.json 3 30 12 200 0 20 1> /data/asap2/users/1/bjtwkg/dim_reduction/24729/exec.out 2> /data/asap2/users/1/bjtwkg/dim_reduction/24729/exec.err'"


## ----------------------------------------------------------------
## Run 24730  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/24730/"

## Running Clustering [24730] [Clustering #1 seurat] (input_matrix:dim_reduction #1)
echo '-> Running Clustering [24730] [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_24730 --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/bjtwkg/gene_filtering/24699/output.loom /data/asap2/users/1/bjtwkg/clustering/24730 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_1_seurat 20 0.8 louvain snn 1> /data/asap2/users/1/bjtwkg/clustering/24730/exec.out 2> /data/asap2/users/1/bjtwkg/clustering/24730/exec.err'"


## ----------------------------------------------------------------
## Run 24731  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/24731/"

## Running Clustering [24731] [Clustering #2 seurat] (input_matrix:dim_reduction #1 Graph type:nn)
echo '-> Running Clustering [24731] [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_24731 --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/bjtwkg/gene_filtering/24699/output.loom /data/asap2/users/1/bjtwkg/clustering/24731 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_2_seurat 20 0.8 louvain nn 1> /data/asap2/users/1/bjtwkg/clustering/24731/exec.out 2> /data/asap2/users/1/bjtwkg/clustering/24731/exec.err'"


## ----------------------------------------------------------------
## Run 24732  Cell selection  (Cell selection #7 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/24732/"

## Running Cell selection [24732] [Cell selection #7 cell_sel] ()
echo '-> Running Cell selection [24732] [Cell selection #7 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/bjtwkg/gene_filtering/24699/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_7 -f /data/asap2/users/1/bjtwkg/metadata/24732/list_cols.json '


## ----------------------------------------------------------------
## Run 24733  Cell selection  (Cell selection #8 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/24733/"

## Running Cell selection [24733] [Cell selection #8 cell_sel] ()
echo '-> Running Cell selection [24733] [Cell selection #8 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/bjtwkg/gene_filtering/24699/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_8 -f /data/asap2/users/1/bjtwkg/metadata/24733/list_cols.json '


## ----------------------------------------------------------------
## Run 24787  Cell selection  (Cell selection #9 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/24787/"

## Running Cell selection [24787] [Cell selection #9 cell_sel] ()
echo '-> Running Cell selection [24787] [Cell selection #9 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/bjtwkg/gene_filtering/24699/output.loom -meta /col_attrs/_dr_7_tsne_scanpy_3D.sel_9 -f /data/asap2/users/1/bjtwkg/metadata/24787/list_cols.json '


## ----------------------------------------------------------------
## Run 24788  Cell selection  (Cell selection #10 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/24788/"

## Running Cell selection [24788] [Cell selection #10 cell_sel] ()
echo '-> Running Cell selection [24788] [Cell selection #10 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/bjtwkg/gene_filtering/24699/output.loom -meta /col_attrs/_dr_7_tsne_scanpy_3D.sel_10 -f /data/asap2/users/1/bjtwkg/metadata/24788/list_cols.json '


## ----------------------------------------------------------------
## Run 24797  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/24797/"

## Running Differential expression [24797] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:11 Compared group:)
echo '-> Running Differential expression [24797] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:11 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_24797 --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/bjtwkg/gene_filtering/24699/output.loom /data/asap2/users/1/bjtwkg/de/24797 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_1_wilcox_seurat null /col_attrs/_clust_1_seurat 11 null false 0.1 null 1.3 null 1> /data/asap2/users/1/bjtwkg/de/24797/exec.out 2> /data/asap2/users/1/bjtwkg/de/24797/exec.err'"


## ----------------------------------------------------------------
## Run 24798  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/24798/"

## Running Differential expression [24798] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:19 Compared group:)
echo '-> Running Differential expression [24798] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:19 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_24798 --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/bjtwkg/gene_filtering/24699/output.loom /data/asap2/users/1/bjtwkg/de/24798 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_2_wilcox_seurat null /col_attrs/_clust_1_seurat 19 null false 0.1 null 1.3 null 1> /data/asap2/users/1/bjtwkg/de/24798/exec.out 2> /data/asap2/users/1/bjtwkg/de/24798/exec.err'"


## ----------------------------------------------------------------
## Run 24799  Differential expression  (Differential expression #3 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/24799/"

## Running Differential expression [24799] [Differential expression #3 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:20 Compared group:)
echo '-> Running Differential expression [24799] [Differential expression #3 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_24799 --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/bjtwkg/gene_filtering/24699/output.loom /data/asap2/users/1/bjtwkg/de/24799 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_3_wilcox_seurat null /col_attrs/_clust_1_seurat 20 null false 0.1 null 1.3 null 1> /data/asap2/users/1/bjtwkg/de/24799/exec.out 2> /data/asap2/users/1/bjtwkg/de/24799/exec.err'"


## ----------------------------------------------------------------
## Run 24800  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/24800/"

## Running Gene Enrichment [24800] [Gene Enrichment #1 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24800] [Gene Enrichment #1 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_24800 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24799_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24800/output.json -max 500 -min 15 -adj fdr -geneset 1719 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24800/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24800/exec.err'"


## ----------------------------------------------------------------
## Run 24801  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/24801/"

## Running Gene Enrichment [24801] [Gene Enrichment #2 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24801] [Gene Enrichment #2 basic] (input_de:de #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_24801 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24798_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24801/output.json -max 500 -min 15 -adj fdr -geneset 1719 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24801/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24801/exec.err'"


## ----------------------------------------------------------------
## Run 24802  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/24802/"

## Running Gene Enrichment [24802] [Gene Enrichment #3 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24802] [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_24802 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24797_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24802/output.json -max 500 -min 15 -adj fdr -geneset 1719 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24802/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24802/exec.err'"


## ----------------------------------------------------------------
## Run 24803  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/24803/"

## Running Gene Enrichment [24803] [Gene Enrichment #4 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24803] [Gene Enrichment #4 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_24803 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24799_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24803/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/1/bjtwkg/ge/24803/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24803/exec.err'"


## ----------------------------------------------------------------
## Run 24804  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/24804/"

## Running Gene Enrichment [24804] [Gene Enrichment #5 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24804] [Gene Enrichment #5 basic] (input_de:de #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_24804 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24798_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24804/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/1/bjtwkg/ge/24804/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24804/exec.err'"


## ----------------------------------------------------------------
## Run 24805  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/24805/"

## Running Gene Enrichment [24805] [Gene Enrichment #6 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24805] [Gene Enrichment #6 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_24805 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24797_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24805/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/1/bjtwkg/ge/24805/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24805/exec.err'"


## ----------------------------------------------------------------
## Run 24806  Gene Enrichment  (Gene Enrichment #7 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/24806/"

## Running Gene Enrichment [24806] [Gene Enrichment #7 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24806] [Gene Enrichment #7 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_24806 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24799_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24806/output.json -max 500 -min 15 -adj fdr -geneset 55 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24806/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24806/exec.err'"


## ----------------------------------------------------------------
## Run 24807  Gene Enrichment  (Gene Enrichment #8 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/24807/"

## Running Gene Enrichment [24807] [Gene Enrichment #8 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24807] [Gene Enrichment #8 basic] (input_de:de #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_24807 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24798_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24807/output.json -max 500 -min 15 -adj fdr -geneset 55 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24807/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24807/exec.err'"


## ----------------------------------------------------------------
## Run 24808  Gene Enrichment  (Gene Enrichment #9 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/24808/"

## Running Gene Enrichment [24808] [Gene Enrichment #9 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24808] [Gene Enrichment #9 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_24808 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24797_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24808/output.json -max 500 -min 15 -adj fdr -geneset 55 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24808/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24808/exec.err'"


## ----------------------------------------------------------------
## Run 24809  Gene Enrichment  (Gene Enrichment #10 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/24809/"

## Running Gene Enrichment [24809] [Gene Enrichment #10 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24809] [Gene Enrichment #10 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_24809 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24799_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24809/output.json -max 500 -min 15 -adj fdr -geneset 53 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24809/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24809/exec.err'"


## ----------------------------------------------------------------
## Run 24810  Gene Enrichment  (Gene Enrichment #11 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/24810/"

## Running Gene Enrichment [24810] [Gene Enrichment #11 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24810] [Gene Enrichment #11 basic] (input_de:de #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_24810 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24798_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24810/output.json -max 500 -min 15 -adj fdr -geneset 53 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24810/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24810/exec.err'"


## ----------------------------------------------------------------
## Run 24811  Gene Enrichment  (Gene Enrichment #12 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/24811/"

## Running Gene Enrichment [24811] [Gene Enrichment #12 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24811] [Gene Enrichment #12 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_24811 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24797_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24811/output.json -max 500 -min 15 -adj fdr -geneset 53 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24811/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24811/exec.err'"


## ----------------------------------------------------------------
## Run 24812  Gene Enrichment  (Gene Enrichment #13 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/24812/"

## Running Gene Enrichment [24812] [Gene Enrichment #13 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24812] [Gene Enrichment #13 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_24812 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24799_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24812/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/bjtwkg/ge/24812/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24812/exec.err'"


## ----------------------------------------------------------------
## Run 24813  Gene Enrichment  (Gene Enrichment #14 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/24813/"

## Running Gene Enrichment [24813] [Gene Enrichment #14 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24813] [Gene Enrichment #14 basic] (input_de:de #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_24813 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24798_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24813/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/bjtwkg/ge/24813/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24813/exec.err'"


## ----------------------------------------------------------------
## Run 24814  Gene Enrichment  (Gene Enrichment #15 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/24814/"

## Running Gene Enrichment [24814] [Gene Enrichment #15 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24814] [Gene Enrichment #15 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_24814 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24797_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24814/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/bjtwkg/ge/24814/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24814/exec.err'"


## ----------------------------------------------------------------
## Run 24815  Gene Enrichment  (Gene Enrichment #16 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/24815/"

## Running Gene Enrichment [24815] [Gene Enrichment #16 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24815] [Gene Enrichment #16 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_24815 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24799_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24815/output.json -max 500 -min 15 -adj fdr -geneset 51 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24815/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24815/exec.err'"


## ----------------------------------------------------------------
## Run 24816  Gene Enrichment  (Gene Enrichment #17 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/24816/"

## Running Gene Enrichment [24816] [Gene Enrichment #17 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24816] [Gene Enrichment #17 basic] (input_de:de #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_24816 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24798_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24816/output.json -max 500 -min 15 -adj fdr -geneset 51 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24816/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24816/exec.err'"


## ----------------------------------------------------------------
## Run 24817  Gene Enrichment  (Gene Enrichment #18 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/24817/"

## Running Gene Enrichment [24817] [Gene Enrichment #18 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24817] [Gene Enrichment #18 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_24817 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24797_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24817/output.json -max 500 -min 15 -adj fdr -geneset 51 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24817/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24817/exec.err'"


## ----------------------------------------------------------------
## Run 24818  Gene Enrichment  (Gene Enrichment #19 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/24818/"

## Running Gene Enrichment [24818] [Gene Enrichment #19 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24818] [Gene Enrichment #19 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_24818 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24799_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24818/output.json -max 500 -min 15 -adj fdr -geneset 1720 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24818/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24818/exec.err'"


## ----------------------------------------------------------------
## Run 24819  Gene Enrichment  (Gene Enrichment #20 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/24819/"

## Running Gene Enrichment [24819] [Gene Enrichment #20 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24819] [Gene Enrichment #20 basic] (input_de:de #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_24819 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24798_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24819/output.json -max 500 -min 15 -adj fdr -geneset 1720 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24819/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24819/exec.err'"


## ----------------------------------------------------------------
## Run 24820  Gene Enrichment  (Gene Enrichment #21 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/24820/"

## Running Gene Enrichment [24820] [Gene Enrichment #21 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24820] [Gene Enrichment #21 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_24820 --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/bjtwkg/gene_filtering/24699/output.loom -m fet -f /data/asap2/users/1/bjtwkg/tmp/1_24797_2_0.05_filtered_ids.json -o /data/asap2/users/1/bjtwkg/ge/24820/output.json -max 500 -min 15 -adj fdr -geneset 1720 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/ge/24820/exec.out 2> /data/asap2/users/1/bjtwkg/ge/24820/exec.err'"


## ----------------------------------------------------------------
## Run 325966  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/325966/"

## Running Find markers [325966] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [325966] [Find markers #1 asap_markers] ()'

## 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_325966 --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/bjtwkg/gene_filtering/24699/output.loom -o /data/asap2/users/1/bjtwkg/markers/325966 --iAnnot /col_attrs/_clust_1_seurat --id 108612 --is_count_table  1> /data/asap2/users/1/bjtwkg/markers/325966/exec.out 2> /data/asap2/users/1/bjtwkg/markers/325966/exec.err'"


## ----------------------------------------------------------------
## Run 325967  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/325967/"

## Running Marker enrichment [325967] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [325967] [Marker enrichment #2 asap_marker_enrichment] ()'

## 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_325967 --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/bjtwkg/markers/325966 -o /data/asap2/users/1/bjtwkg/markers/325967 --genesets 52,55,53,1719,1720,51,2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/bjtwkg/markers/325967/exec.out 2> /data/asap2/users/1/bjtwkg/markers/325967/exec.err'"