## This script contains all commands executed in the PROJECT ymjqvi and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT ymjqvi / ASAP7**********************'
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/ymjqvi
## 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/"

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

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


## ----------------------------------------------------------------
## Run 15297  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/15297/"

## writing file $PROJECT_DIR/cell_filtering/15297/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/15297/discarded_cols.json'
## writing file $PROJECT_DIR/cell_filtering/15297/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/15297/manually_discarded_cols.json'
## Running Cell filtering [15297] [Cell filtering #1 qc_plots] (Depth:100 Detected genes:10 Protein coding content:80 Mito content:100 Ribo content:20 Nber manually discarded cols:0 input_matrix:parsing)
echo '-> Running Cell filtering [15297] [Cell filtering #1 qc_plots] (Depth:100 Detected genes:10 Protein coding content:80 Mito content:100 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_15297 --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/ymjqvi/parsing/output.loom -o /data/asap2/users/1/ymjqvi/cell_filtering/15297 -col_indexes_file /data/asap2/users/1/ymjqvi/cell_filtering/15297/discarded_cols.json  1> /data/asap2/users/1/ymjqvi/cell_filtering/15297/exec.out 2> /data/asap2/users/1/ymjqvi/cell_filtering/15297/exec.err'"


## ----------------------------------------------------------------
## Run 15303  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/15303/"

## Running Gene filtering [15303] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [15303] [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_15303 --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/ymjqvi/cell_filtering/15297/output.loom /matrix /data/asap2/users/1/ymjqvi/gene_filtering/15303 0.5 0.0125 3 Inf 20 None false 1> /data/asap2/users/1/ymjqvi/gene_filtering/15303/exec.out 2> /data/asap2/users/1/ymjqvi/gene_filtering/15303/exec.err'"


## ----------------------------------------------------------------
## Run 15311  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/15311/"

## Running Normalization [15311] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1)
echo '-> Running Normalization [15311] [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_15311 --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/ymjqvi/gene_filtering/15303/output.loom -o /data/asap2/users/1/ymjqvi/normalization/15311/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/ymjqvi/normalization/15311/exec.out 2> /data/asap2/users/1/ymjqvi/normalization/15311/exec.err'"


## ----------------------------------------------------------------
## Run 15312  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/15312/"

## Running Normalization [15312] [Normalization #2 asap_seurat] (input_matrix:cell_filtering #1)
echo '-> Running Normalization [15312] [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_15312 --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/ymjqvi/cell_filtering/15297/output.loom -o /data/asap2/users/1/ymjqvi/normalization/15312/output.json -oAnnot /layers/norm_2_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/ymjqvi/normalization/15312/exec.out 2> /data/asap2/users/1/ymjqvi/normalization/15312/exec.err'"


## ----------------------------------------------------------------
## Run 15314  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/15314/"

## Running Scaling [15314] [Scaling #1 asap_seurat] (input_matrix:normalization #1)
echo '-> Running Scaling [15314] [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_15314 --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/ymjqvi/gene_filtering/15303/output.loom -o /data/asap2/users/1/ymjqvi/scaling/15314/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/ymjqvi/scaling/15314/exec.out 2> /data/asap2/users/1/ymjqvi/scaling/15314/exec.err'"


## ----------------------------------------------------------------
## Run 15315  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/15315/"

## Running Dimension reduction [15315] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1)
echo '-> Running Dimension reduction [15315] [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_15315 --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/ymjqvi/gene_filtering/15303/output.loom /layers/scaling_1_asap_seurat /col_attrs/_dr_1_inc_pca_50D /data/asap2/users/1/ymjqvi/dim_reduction/15315/output.json 50 10000 20 1> /data/asap2/users/1/ymjqvi/dim_reduction/15315/exec.out 2> /data/asap2/users/1/ymjqvi/dim_reduction/15315/exec.err'"


## ----------------------------------------------------------------
## Run 15320  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/15320/"

## Running Dimension reduction [15320] [Dimension reduction #4 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:2 Perplexity:500)
echo '-> Running Dimension reduction [15320] [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_15320 --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/ymjqvi/gene_filtering/15303/output.loom /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_4_tsne_scanpy_2D /data/asap2/users/1/ymjqvi/dim_reduction/15320/output.json 2 500 12 200 0 20 1> /data/asap2/users/1/ymjqvi/dim_reduction/15320/exec.out 2> /data/asap2/users/1/ymjqvi/dim_reduction/15320/exec.err'"


## ----------------------------------------------------------------
## Run 15321  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/15321/"

## Running Dimension reduction [15321] [Dimension reduction #5 tsne_scanpy] (input_matrix:dim_reduction #1 Number of dimensions:3 Perplexity:500)
echo '-> Running Dimension reduction [15321] [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_15321 --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/ymjqvi/gene_filtering/15303/output.loom /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_5_tsne_scanpy_3D /data/asap2/users/1/ymjqvi/dim_reduction/15321/output.json 3 500 12 200 0 20 1> /data/asap2/users/1/ymjqvi/dim_reduction/15321/exec.out 2> /data/asap2/users/1/ymjqvi/dim_reduction/15321/exec.err'"


## ----------------------------------------------------------------
## Run 16144  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/16144/"

## Running Clustering [16144] [Clustering #1 seurat] (input_matrix:dim_reduction #1 k:100 Resolution:0.5 Graph type:nn)
echo '-> Running Clustering [16144] [Clustering #1 seurat] (input_matrix:dim_reduction #1 k:100 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_16144 --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/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/clustering/16144 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_1_seurat 100 0.5 louvain nn 1> /data/asap2/users/1/ymjqvi/clustering/16144/exec.out 2> /data/asap2/users/1/ymjqvi/clustering/16144/exec.err'"


## ----------------------------------------------------------------
## Run 16154  Dimension reduction  (Dimension reduction #6 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/16154/"

## Running Dimension reduction [16154] [Dimension reduction #6 umap] (input_matrix:dim_reduction #1 Number of dimensions:2 Min distance:0.05)
echo '-> Running Dimension reduction [16154] [Dimension reduction #6 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_16154 --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/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/dim_reduction/16154 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_6_umap_2D 2 0.05 30 correlation 1> /data/asap2/users/1/ymjqvi/dim_reduction/16154/exec.out 2> /data/asap2/users/1/ymjqvi/dim_reduction/16154/exec.err'"


## ----------------------------------------------------------------
## Run 16155  Dimension reduction  (Dimension reduction #7 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/16155/"

## Running Dimension reduction [16155] [Dimension reduction #7 umap] (input_matrix:dim_reduction #1 Number of dimensions:3 Min distance:0.05)
echo '-> Running Dimension reduction [16155] [Dimension reduction #7 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_16155 --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/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/dim_reduction/16155 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_7_umap_3D 3 0.05 30 correlation 1> /data/asap2/users/1/ymjqvi/dim_reduction/16155/exec.out 2> /data/asap2/users/1/ymjqvi/dim_reduction/16155/exec.err'"


## ----------------------------------------------------------------
## Run 24222  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/24222/"

## Running Differential expression [24222] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:9 Compared group:)
echo '-> Running Differential expression [24222] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:9 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_24222 --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/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/de/24222 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_1_wilcox_seurat null /col_attrs/_clust_1_seurat 9 null false 0.1 null 1.3 null 1> /data/asap2/users/1/ymjqvi/de/24222/exec.out 2> /data/asap2/users/1/ymjqvi/de/24222/exec.err'"


## ----------------------------------------------------------------
## Run 24224  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/24224/"

## Running Differential expression [24224] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:12 Compared group:)
echo '-> Running Differential expression [24224] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:12 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_24224 --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/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/de/24224 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_2_wilcox_seurat null /col_attrs/_clust_1_seurat 12 null false 0.1 null 1.3 null 1> /data/asap2/users/1/ymjqvi/de/24224/exec.out 2> /data/asap2/users/1/ymjqvi/de/24224/exec.err'"


## ----------------------------------------------------------------
## Run 24225  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/24225/"

## Running Differential expression [24225] [Differential expression #3 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:6 Compared group:)
echo '-> Running Differential expression [24225] [Differential expression #3 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 Reference group:6 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_24225 --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/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/de/24225 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_3_wilcox_seurat null /col_attrs/_clust_1_seurat 6 null false 0.1 null 1.3 null 1> /data/asap2/users/1/ymjqvi/de/24225/exec.out 2> /data/asap2/users/1/ymjqvi/de/24225/exec.err'"


## ----------------------------------------------------------------
## Run 24228  Differential expression  (Differential expression #4 wilcox_asap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/24228/"

## Running Differential expression [24228] [Differential expression #4 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:12 Compared group:)
echo '-> Running Differential expression [24228] [Differential expression #4 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:12 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_24228 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T DifferentialExpression -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -o /data/asap2/users/1/ymjqvi/de/24228 -m wilcox_asap -iAnnot /layers/norm_1_asap_seurat -oAnnot /row_attrs/_de_4_wilcox_asap -gAnnot /col_attrs/_clust_1_seurat -g1 12 -g2 null  1> /data/asap2/users/1/ymjqvi/de/24228/exec.out 2> /data/asap2/users/1/ymjqvi/de/24228/exec.err'"


## ----------------------------------------------------------------
## Run 24229  Differential expression  (Differential expression #5 wilcox_asap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/24229/"

## Running Differential expression [24229] [Differential expression #5 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:6 Compared group:)
echo '-> Running Differential expression [24229] [Differential expression #5 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:6 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_24229 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T DifferentialExpression -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -o /data/asap2/users/1/ymjqvi/de/24229 -m wilcox_asap -iAnnot /layers/norm_1_asap_seurat -oAnnot /row_attrs/_de_5_wilcox_asap -gAnnot /col_attrs/_clust_1_seurat -g1 6 -g2 null  1> /data/asap2/users/1/ymjqvi/de/24229/exec.out 2> /data/asap2/users/1/ymjqvi/de/24229/exec.err'"


## ----------------------------------------------------------------
## Run 24230  Differential expression  (Differential expression #6 wilcox_asap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/24230/"

## Running Differential expression [24230] [Differential expression #6 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:9 Compared group:)
echo '-> Running Differential expression [24230] [Differential expression #6 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 Reference group:9 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_24230 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T DifferentialExpression -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -o /data/asap2/users/1/ymjqvi/de/24230 -m wilcox_asap -iAnnot /layers/norm_1_asap_seurat -oAnnot /row_attrs/_de_6_wilcox_asap -gAnnot /col_attrs/_clust_1_seurat -g1 9 -g2 null  1> /data/asap2/users/1/ymjqvi/de/24230/exec.out 2> /data/asap2/users/1/ymjqvi/de/24230/exec.err'"


## ----------------------------------------------------------------
## Run 24234  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/24234/"

## Running Gene Enrichment [24234] [Gene Enrichment #1 basic] (input_de:de #6)
echo '-> Running Gene Enrichment [24234] [Gene Enrichment #1 basic] (input_de:de #6)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_24234 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24230_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24234/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/ymjqvi/ge/24234/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24234/exec.err'"


## ----------------------------------------------------------------
## Run 24235  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/24235/"

## Running Gene Enrichment [24235] [Gene Enrichment #2 basic] (input_de:de #5)
echo '-> Running Gene Enrichment [24235] [Gene Enrichment #2 basic] (input_de:de #5)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_24235 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24229_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24235/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/ymjqvi/ge/24235/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24235/exec.err'"


## ----------------------------------------------------------------
## Run 24236  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/24236/"

## Running Gene Enrichment [24236] [Gene Enrichment #3 basic] (input_de:de #4)
echo '-> Running Gene Enrichment [24236] [Gene Enrichment #3 basic] (input_de:de #4)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_24236 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24228_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24236/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/ymjqvi/ge/24236/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24236/exec.err'"


## ----------------------------------------------------------------
## Run 24237  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/24237/"

## Running Gene Enrichment [24237] [Gene Enrichment #4 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24237] [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_24237 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24225_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24237/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/ymjqvi/ge/24237/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24237/exec.err'"


## ----------------------------------------------------------------
## Run 24238  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/24238/"

## Running Gene Enrichment [24238] [Gene Enrichment #5 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24238] [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_24238 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24224_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24238/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/ymjqvi/ge/24238/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24238/exec.err'"


## ----------------------------------------------------------------
## Run 24239  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/24239/"

## Running Gene Enrichment [24239] [Gene Enrichment #6 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24239] [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_24239 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24222_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24239/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/ymjqvi/ge/24239/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24239/exec.err'"


## ----------------------------------------------------------------
## Run 24240  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/24240/"

## Running Gene Enrichment [24240] [Gene Enrichment #7 basic] (input_de:de #6)
echo '-> Running Gene Enrichment [24240] [Gene Enrichment #7 basic] (input_de:de #6)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_24240 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24230_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24240/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/ymjqvi/ge/24240/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24240/exec.err'"


## ----------------------------------------------------------------
## Run 24241  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/24241/"

## Running Gene Enrichment [24241] [Gene Enrichment #8 basic] (input_de:de #5)
echo '-> Running Gene Enrichment [24241] [Gene Enrichment #8 basic] (input_de:de #5)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_24241 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24229_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24241/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/ymjqvi/ge/24241/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24241/exec.err'"


## ----------------------------------------------------------------
## Run 24242  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/24242/"

## Running Gene Enrichment [24242] [Gene Enrichment #9 basic] (input_de:de #4)
echo '-> Running Gene Enrichment [24242] [Gene Enrichment #9 basic] (input_de:de #4)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_24242 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24228_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24242/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/ymjqvi/ge/24242/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24242/exec.err'"


## ----------------------------------------------------------------
## Run 24243  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/24243/"

## Running Gene Enrichment [24243] [Gene Enrichment #10 basic] (input_de:de #3)
echo '-> Running Gene Enrichment [24243] [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_24243 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24225_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24243/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/ymjqvi/ge/24243/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24243/exec.err'"


## ----------------------------------------------------------------
## Run 24244  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/24244/"

## Running Gene Enrichment [24244] [Gene Enrichment #11 basic] (input_de:de #2)
echo '-> Running Gene Enrichment [24244] [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_24244 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24224_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24244/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/ymjqvi/ge/24244/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24244/exec.err'"


## ----------------------------------------------------------------
## Run 24245  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/24245/"

## Running Gene Enrichment [24245] [Gene Enrichment #12 basic] (input_de:de #1)
echo '-> Running Gene Enrichment [24245] [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_24245 --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/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24222_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24245/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/ymjqvi/ge/24245/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24245/exec.err'"