## This script contains all commands executed in the PROJECT zwy667 and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT zwy667 / ASAP8**********************'
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/zwy667
## 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/parsing/ && mkdir -p $PROJECT_DIR/dim_reduction/ && mkdir -p $PROJECT_DIR/cell_selection/"

## 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/zwy667/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 15296  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/15296/"

## writing file $PROJECT_DIR/cell_filtering/15296/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/15296/discarded_cols.json'
## writing file $PROJECT_DIR/cell_filtering/15296/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/15296/manually_discarded_cols.json'
## Running Cell filtering [15296] [Cell filtering #1 qc_plots] (Depth:100 Detected genes:10 Protein coding content:80 Mito content:40 Ribo content:40 Nber manually discarded cols:0 input_matrix:parsing)
echo '-> Running Cell filtering [15296] [Cell filtering #1 qc_plots] (Depth:100 Detected genes:10 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_15296 --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/zwy667/parsing/output.loom -o /data/asap2/users/1/zwy667/cell_filtering/15296 -col_indexes_file /data/asap2/users/1/zwy667/cell_filtering/15296/discarded_cols.json  1> /data/asap2/users/1/zwy667/cell_filtering/15296/exec.out 2> /data/asap2/users/1/zwy667/cell_filtering/15296/exec.err'"


## ----------------------------------------------------------------
## Run 15298  Gene filtering  (Gene filtering #1 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/15298/"

## Running Gene filtering [15298] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [15298] [Gene filtering #1 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_15298 --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/zwy667/cell_filtering/15296/output.loom /matrix /data/asap2/users/1/zwy667/gene_filtering/15298 0.5 0.0125 3 Inf 20 None false 1> /data/asap2/users/1/zwy667/gene_filtering/15298/exec.out 2> /data/asap2/users/1/zwy667/gene_filtering/15298/exec.err'"


## ----------------------------------------------------------------
## Run 15299  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/15299/"

## Running Normalization [15299] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1)
echo '-> Running Normalization [15299] [Normalization #1 asap_seurat] (input_matrix:gene_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_15299 --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/zwy667/gene_filtering/15298/output.loom -o /data/asap2/users/1/zwy667/normalization/15299/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/zwy667/normalization/15299/exec.out 2> /data/asap2/users/1/zwy667/normalization/15299/exec.err'"


## ----------------------------------------------------------------
## Run 15300  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/15300/"

## Running Scaling [15300] [Scaling #1 asap_seurat] (input_matrix:normalization #1)
echo '-> Running Scaling [15300] [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_15300 --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/zwy667/gene_filtering/15298/output.loom -o /data/asap2/users/1/zwy667/scaling/15300/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/zwy667/scaling/15300/exec.out 2> /data/asap2/users/1/zwy667/scaling/15300/exec.err'"


## ----------------------------------------------------------------
## Run 15301  Normalization  (Normalization #2 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/15301/"

## Running Normalization [15301] [Normalization #2 asap_seurat] (input_matrix:cell_filtering #1)
echo '-> Running Normalization [15301] [Normalization #2 asap_seurat] (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_15301 --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/zwy667/cell_filtering/15296/output.loom -o /data/asap2/users/1/zwy667/normalization/15301/output.json -oAnnot /layers/norm_2_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/zwy667/normalization/15301/exec.out 2> /data/asap2/users/1/zwy667/normalization/15301/exec.err'"


## ----------------------------------------------------------------
## Run 15304  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/15304/"

## Running Dimension reduction [15304] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1)
echo '-> Running Dimension reduction [15304] [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_15304 --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/zwy667/gene_filtering/15298/output.loom /layers/scaling_1_asap_seurat /col_attrs/_dr_1_inc_pca_50D /data/asap2/users/1/zwy667/dim_reduction/15304/output.json 50 10000 20 1> /data/asap2/users/1/zwy667/dim_reduction/15304/exec.out 2> /data/asap2/users/1/zwy667/dim_reduction/15304/exec.err'"


## ----------------------------------------------------------------
## Run 15307  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/15307/"

## Running Dimension reduction [15307] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 Number of dimensions:2 Min distance:0.05)
echo '-> Running Dimension reduction [15307] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 Number of dimensions:2 Min distance:0.05)'

## 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_15307 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/dim_reduction/15307 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_2_umap_2D 2 0.05 30 correlation 1> /data/asap2/users/1/zwy667/dim_reduction/15307/exec.out 2> /data/asap2/users/1/zwy667/dim_reduction/15307/exec.err'"


## ----------------------------------------------------------------
## Run 15308  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/15308/"

## Running Dimension reduction [15308] [Dimension reduction #3 umap] (input_matrix:dim_reduction #1 Number of dimensions:3 Min distance:0.05)
echo '-> Running Dimension reduction [15308] [Dimension reduction #3 umap] (input_matrix:dim_reduction #1 Number of dimensions:3 Min distance:0.05)'

## 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_15308 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/dim_reduction/15308 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_3_umap_3D 3 0.05 30 correlation 1> /data/asap2/users/1/zwy667/dim_reduction/15308/exec.out 2> /data/asap2/users/1/zwy667/dim_reduction/15308/exec.err'"


## ----------------------------------------------------------------
## Run 15309  Dimension reduction  (Dimension reduction #4 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/15309/"

## Running Dimension reduction [15309] [Dimension reduction #4 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:2 Perplexity:500)
echo '-> Running Dimension reduction [15309] [Dimension reduction #4 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:2 Perplexity:500)'

## 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_15309 --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/zwy667/gene_filtering/15298/output.loom /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_4_tsne_scanpy_2D /data/asap2/users/1/zwy667/dim_reduction/15309/output.json 2 500 12 200 0 20 1> /data/asap2/users/1/zwy667/dim_reduction/15309/exec.out 2> /data/asap2/users/1/zwy667/dim_reduction/15309/exec.err'"


## ----------------------------------------------------------------
## Run 15310  Dimension reduction  (Dimension reduction #5 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/15310/"

## Running Dimension reduction [15310] [Dimension reduction #5 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:3 Perplexity:500)
echo '-> Running Dimension reduction [15310] [Dimension reduction #5 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:3 Perplexity:500)'

## 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_15310 --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/zwy667/gene_filtering/15298/output.loom /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_5_tsne_scanpy_3D /data/asap2/users/1/zwy667/dim_reduction/15310/output.json 3 500 12 200 0 20 1> /data/asap2/users/1/zwy667/dim_reduction/15310/exec.out 2> /data/asap2/users/1/zwy667/dim_reduction/15310/exec.err'"


## ----------------------------------------------------------------
## Run 16127  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/16127/"

## Running Clustering [16127] [Clustering #1 seurat] (input_matrix:dim_reduction #1)
echo '-> Running Clustering [16127] [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_16127 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/clustering/16127 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_1_seurat 20 0.8 louvain snn 1> /data/asap2/users/1/zwy667/clustering/16127/exec.out 2> /data/asap2/users/1/zwy667/clustering/16127/exec.err'"


## ----------------------------------------------------------------
## Run 16533  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/16533/"

## Running Clustering [16533] [Clustering #2 seurat] (input_matrix:dim_reduction #1 k:30 Resolution:0.5 Graph type:nn)
echo '-> Running Clustering [16533] [Clustering #2 seurat] (input_matrix:dim_reduction #1 k:30 Resolution:0.5 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_16533 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/clustering/16533 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_2_seurat 30 0.5 louvain nn 1> /data/asap2/users/1/zwy667/clustering/16533/exec.out 2> /data/asap2/users/1/zwy667/clustering/16533/exec.err'"


## ----------------------------------------------------------------
## Run 16534  Clustering  (Clustering #3 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/16534/"

## Running Clustering [16534] [Clustering #3 seurat] (input_matrix:dim_reduction #1 k:30 Resolution:0.5)
echo '-> Running Clustering [16534] [Clustering #3 seurat] (input_matrix:dim_reduction #1 k:30 Resolution:0.5)'

## 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_16534 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/clustering/16534 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_3_seurat 30 0.5 louvain snn 1> /data/asap2/users/1/zwy667/clustering/16534/exec.out 2> /data/asap2/users/1/zwy667/clustering/16534/exec.err'"


## ----------------------------------------------------------------
## Run 16535  Clustering  (Clustering #4 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/16535/"

## Running Clustering [16535] [Clustering #4 seurat] (input_matrix:dim_reduction #1 k:40 Resolution:0.5)
echo '-> Running Clustering [16535] [Clustering #4 seurat] (input_matrix:dim_reduction #1 k:40 Resolution:0.5)'

## 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_16535 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/clustering/16535 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_4_seurat 40 0.5 louvain snn 1> /data/asap2/users/1/zwy667/clustering/16535/exec.out 2> /data/asap2/users/1/zwy667/clustering/16535/exec.err'"


## ----------------------------------------------------------------
## Run 16536  Clustering  (Clustering #5 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/16536/"

## Running Clustering [16536] [Clustering #5 seurat] (input_matrix:dim_reduction #1 k:50 Resolution:0.5)
echo '-> Running Clustering [16536] [Clustering #5 seurat] (input_matrix:dim_reduction #1 k:50 Resolution:0.5)'

## 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_16536 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/clustering/16536 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_5_seurat 50 0.5 louvain snn 1> /data/asap2/users/1/zwy667/clustering/16536/exec.out 2> /data/asap2/users/1/zwy667/clustering/16536/exec.err'"


## ----------------------------------------------------------------
## Run 16537  Clustering  (Clustering #6 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/16537/"

## Running Clustering [16537] [Clustering #6 seurat] (input_matrix:dim_reduction #1 k:50 Resolution:0.5 Graph type:nn)
echo '-> Running Clustering [16537] [Clustering #6 seurat] (input_matrix:dim_reduction #1 k:50 Resolution:0.5 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_16537 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/clustering/16537 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_6_seurat 50 0.5 louvain nn 1> /data/asap2/users/1/zwy667/clustering/16537/exec.out 2> /data/asap2/users/1/zwy667/clustering/16537/exec.err'"


## ----------------------------------------------------------------
## Run 16538  Clustering  (Clustering #7 kmeans)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/clustering/16538/"

## Running Clustering [16538] [Clustering #7 kmeans] (input_matrix:dim_reduction #1 Number of clusters:30)
echo '-> Running Clustering [16538] [Clustering #7 kmeans] (input_matrix:dim_reduction #1 Number of clusters:30)'

## 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_16538 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/clustering/16538 kmeans /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_7_kmeans 30 Hartigan-Wong 1> /data/asap2/users/1/zwy667/clustering/16538/exec.out 2> /data/asap2/users/1/zwy667/clustering/16538/exec.err'"


## ----------------------------------------------------------------
## Run 16547  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/16547/"

## Running Cell selection [16547] [Cell selection #1 cell_sel] ()
echo '-> Running Cell selection [16547] [Cell selection #1 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/zwy667/gene_filtering/15298/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_1 -f /data/asap2/users/1/zwy667/metadata/16547/list_cols.json '


## ----------------------------------------------------------------
## Run 16548  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/16548/"

## Running Cell selection [16548] [Cell selection #2 cell_sel] ()
echo '-> Running Cell selection [16548] [Cell selection #2 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/zwy667/gene_filtering/15298/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_2 -f /data/asap2/users/1/zwy667/metadata/16548/list_cols.json '


## ----------------------------------------------------------------
## Run 16549  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/16549/"

## Running Cell selection [16549] [Cell selection #3 cell_sel] ()
echo '-> Running Cell selection [16549] [Cell selection #3 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/zwy667/gene_filtering/15298/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_3 -f /data/asap2/users/1/zwy667/metadata/16549/list_cols.json '


## ----------------------------------------------------------------
## Run 16550  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/16550/"

## Running Cell selection [16550] [Cell selection #4 cell_sel] ()
echo '-> Running Cell selection [16550] [Cell selection #4 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/zwy667/gene_filtering/15298/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_4 -f /data/asap2/users/1/zwy667/metadata/16550/list_cols.json '


## ----------------------------------------------------------------
## Run 16551  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/16551/"

## Running Cell selection [16551] [Cell selection #5 cell_sel] ()
echo '-> Running Cell selection [16551] [Cell selection #5 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/zwy667/gene_filtering/15298/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_5 -f /data/asap2/users/1/zwy667/metadata/16551/list_cols.json '


## ----------------------------------------------------------------
## Run 16552  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/16552/"

## Running Cell selection [16552] [Cell selection #6 cell_sel] ()
echo '-> Running Cell selection [16552] [Cell selection #6 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/zwy667/gene_filtering/15298/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_6 -f /data/asap2/users/1/zwy667/metadata/16552/list_cols.json '


## ----------------------------------------------------------------
## Run 24246  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/24246/"

## Running Differential expression [24246] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:13 Compared group:)
echo '-> Running Differential expression [24246] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:13 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_24246 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/de/24246 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_1_wilcox_seurat null /col_attrs/_clust_1_seurat 13 null false 0.1 null 1.3 null 1> /data/asap2/users/1/zwy667/de/24246/exec.out 2> /data/asap2/users/1/zwy667/de/24246/exec.err'"


## ----------------------------------------------------------------
## Run 24247  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/24247/"

## Running Differential expression [24247] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:cell_selection #6 Reference group:1 Compared group:0)
echo '-> Running Differential expression [24247] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:cell_selection #6 Reference group:1 Compared group:0)'

## 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_24247 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/de/24247 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_2_wilcox_seurat null /col_attrs/_dr_2_umap_2D.sel_6 1 0 false 0.1 null 1.3 null 1> /data/asap2/users/1/zwy667/de/24247/exec.out 2> /data/asap2/users/1/zwy667/de/24247/exec.err'"


## ----------------------------------------------------------------
## Run 24248  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/24248/"

## Running Differential expression [24248] [Differential expression #3 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #7 Reference group:1 Compared group:)
echo '-> Running Differential expression [24248] [Differential expression #3 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #7 Reference group:1 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_24248 --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/zwy667/gene_filtering/15298/output.loom /data/asap2/users/1/zwy667/de/24248 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_3_wilcox_seurat null /col_attrs/_clust_7_kmeans 1 null false 0.1 null 1.3 null 1> /data/asap2/users/1/zwy667/de/24248/exec.out 2> /data/asap2/users/1/zwy667/de/24248/exec.err'"


## ----------------------------------------------------------------
## Run 24250  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/24250/"

## Running Gene Enrichment [24250] [Gene Enrichment #1 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24250] [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_24250 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24248_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24250/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/zwy667/ge/24250/exec.out 2> /data/asap2/users/1/zwy667/ge/24250/exec.err'"


## ----------------------------------------------------------------
## Run 24251  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/24251/"

## Running Gene Enrichment [24251] [Gene Enrichment #2 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24251] [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_24251 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24247_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24251/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/zwy667/ge/24251/exec.out 2> /data/asap2/users/1/zwy667/ge/24251/exec.err'"


## ----------------------------------------------------------------
## Run 24252  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/24252/"

## Running Gene Enrichment [24252] [Gene Enrichment #3 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24252] [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_24252 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24246_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24252/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/zwy667/ge/24252/exec.out 2> /data/asap2/users/1/zwy667/ge/24252/exec.err'"


## ----------------------------------------------------------------
## Run 24253  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/24253/"

## Running Gene Enrichment [24253] [Gene Enrichment #4 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24253] [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_24253 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24248_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24253/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/zwy667/ge/24253/exec.out 2> /data/asap2/users/1/zwy667/ge/24253/exec.err'"


## ----------------------------------------------------------------
## Run 24254  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/24254/"

## Running Gene Enrichment [24254] [Gene Enrichment #5 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24254] [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_24254 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24247_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24254/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/zwy667/ge/24254/exec.out 2> /data/asap2/users/1/zwy667/ge/24254/exec.err'"


## ----------------------------------------------------------------
## Run 24255  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/24255/"

## Running Gene Enrichment [24255] [Gene Enrichment #6 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24255] [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_24255 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24246_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24255/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/zwy667/ge/24255/exec.out 2> /data/asap2/users/1/zwy667/ge/24255/exec.err'"


## ----------------------------------------------------------------
## Run 24256  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/24256/"

## Running Gene Enrichment [24256] [Gene Enrichment #7 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24256] [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_24256 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24248_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24256/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/zwy667/ge/24256/exec.out 2> /data/asap2/users/1/zwy667/ge/24256/exec.err'"


## ----------------------------------------------------------------
## Run 24257  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/24257/"

## Running Gene Enrichment [24257] [Gene Enrichment #8 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24257] [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_24257 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24247_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24257/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/zwy667/ge/24257/exec.out 2> /data/asap2/users/1/zwy667/ge/24257/exec.err'"


## ----------------------------------------------------------------
## Run 24258  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/24258/"

## Running Gene Enrichment [24258] [Gene Enrichment #9 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24258] [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_24258 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24246_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24258/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/zwy667/ge/24258/exec.out 2> /data/asap2/users/1/zwy667/ge/24258/exec.err'"


## ----------------------------------------------------------------
## Run 24259  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/24259/"

## Running Gene Enrichment [24259] [Gene Enrichment #10 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24259] [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_24259 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24248_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24259/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/zwy667/ge/24259/exec.out 2> /data/asap2/users/1/zwy667/ge/24259/exec.err'"


## ----------------------------------------------------------------
## Run 24260  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/24260/"

## Running Gene Enrichment [24260] [Gene Enrichment #11 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24260] [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_24260 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24247_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24260/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/zwy667/ge/24260/exec.out 2> /data/asap2/users/1/zwy667/ge/24260/exec.err'"


## ----------------------------------------------------------------
## Run 24261  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/24261/"

## Running Gene Enrichment [24261] [Gene Enrichment #12 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24261] [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_24261 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24246_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24261/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/zwy667/ge/24261/exec.out 2> /data/asap2/users/1/zwy667/ge/24261/exec.err'"


## ----------------------------------------------------------------
## Run 24262  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/24262/"

## Running Gene Enrichment [24262] [Gene Enrichment #13 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24262] [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_24262 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24248_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24262/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/zwy667/ge/24262/exec.out 2> /data/asap2/users/1/zwy667/ge/24262/exec.err'"


## ----------------------------------------------------------------
## Run 24263  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/24263/"

## Running Gene Enrichment [24263] [Gene Enrichment #14 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24263] [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_24263 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24247_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24263/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/zwy667/ge/24263/exec.out 2> /data/asap2/users/1/zwy667/ge/24263/exec.err'"


## ----------------------------------------------------------------
## Run 24264  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/24264/"

## Running Gene Enrichment [24264] [Gene Enrichment #15 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24264] [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_24264 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24246_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24264/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/zwy667/ge/24264/exec.out 2> /data/asap2/users/1/zwy667/ge/24264/exec.err'"


## ----------------------------------------------------------------
## Run 24265  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/24265/"

## Running Gene Enrichment [24265] [Gene Enrichment #16 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24265] [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_24265 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24248_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24265/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/zwy667/ge/24265/exec.out 2> /data/asap2/users/1/zwy667/ge/24265/exec.err'"


## ----------------------------------------------------------------
## Run 24266  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/24266/"

## Running Gene Enrichment [24266] [Gene Enrichment #17 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24266] [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_24266 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24247_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24266/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/zwy667/ge/24266/exec.out 2> /data/asap2/users/1/zwy667/ge/24266/exec.err'"


## ----------------------------------------------------------------
## Run 24267  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/24267/"

## Running Gene Enrichment [24267] [Gene Enrichment #18 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24267] [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_24267 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24246_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24267/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/zwy667/ge/24267/exec.out 2> /data/asap2/users/1/zwy667/ge/24267/exec.err'"


## ----------------------------------------------------------------
## Run 24268  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/24268/"

## Running Gene Enrichment [24268] [Gene Enrichment #19 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24268] [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_24268 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24248_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24268/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/zwy667/ge/24268/exec.out 2> /data/asap2/users/1/zwy667/ge/24268/exec.err'"


## ----------------------------------------------------------------
## Run 24269  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/24269/"

## Running Gene Enrichment [24269] [Gene Enrichment #20 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24269] [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_24269 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24247_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24269/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/zwy667/ge/24269/exec.out 2> /data/asap2/users/1/zwy667/ge/24269/exec.err'"


## ----------------------------------------------------------------
## Run 24270  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/24270/"

## Running Gene Enrichment [24270] [Gene Enrichment #21 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24270] [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_24270 --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/zwy667/gene_filtering/15298/output.loom -m fet -f /data/asap2/users/1/zwy667/tmp/1_24246_2_0.05_filtered_ids.json -o /data/asap2/users/1/zwy667/ge/24270/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/zwy667/ge/24270/exec.out 2> /data/asap2/users/1/zwy667/ge/24270/exec.err'"