## This script contains all commands executed in the PROJECT xj31a6 and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT xj31a6 / ASAP3**********************'
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/xj31a6
## Pull Docker images (must run before any docker run in this script)

docker pull fabdavid/asap_run:v4

## Host LOOM staging directory (inside Docker volume)
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -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_v4; then echo 'Create database asap_data_v4'; echo '$PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v4'; $PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v4; echo 'wget -qO - https://asap.epfl.ch/dumps/asap_data_v4.sql.gz | gunzip | grep -v \'AS integer\' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v4'; wget -qO - https://asap.epfl.ch/dumps/asap_data_v4.sql.gz | gunzip | grep -v 'AS integer' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v4; fi

## Project directory on the shared volume
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -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:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/ && mkdir -p $PROJECT_DIR/normalization/ && mkdir -p $PROJECT_DIR/scaling/ && mkdir -p $PROJECT_DIR/parsing/ && mkdir -p $PROJECT_DIR/clustering/ && mkdir -p $PROJECT_DIR/gene_filtering/ && mkdir -p $PROJECT_DIR/cell_filtering/ && mkdir -p $PROJECT_DIR/de/ && mkdir -p $PROJECT_DIR/markers/"

## Parsed LOOM file (public: wget; private: place file then symlink as below)
echo 'Loading parsed Loom file...'
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "wget -qO $PROJECT_DIR/parsing/output.loom 'https://asap.epfl.ch/projects/xj31a6/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 11098  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:v4 -c "mkdir -p $PROJECT_DIR/cell_filtering/11098/"

## writing file $PROJECT_DIR/cell_filtering/11098/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/11098/discarded_cols.json'
## writing file $PROJECT_DIR/cell_filtering/11098/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/11098/manually_discarded_cols.json'
## Running Cell filtering [11098] [Cell filtering #1 qc_plots] (Depth:100 Detected genes:100 Protein coding content:40 Mito content:40 Ribo content:40 Nber manually discarded cols:0 input_matrix:parsing)
echo '-> Running Cell filtering [11098] [Cell filtering #1 qc_plots] (Depth:100 Detected genes:100 Protein coding content:40 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_11098 --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:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T FilterCols -loom /data/asap2/users/1/xj31a6/parsing/output.loom -o /data/asap2/users/1/xj31a6/cell_filtering/11098 -col_indexes_file /data/asap2/users/1/xj31a6/cell_filtering/11098/discarded_cols.json  1> /data/asap2/users/1/xj31a6/cell_filtering/11098/exec.out 2> /data/asap2/users/1/xj31a6/cell_filtering/11098/exec.err'"


## ----------------------------------------------------------------
## Run 11121  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:v4 -c "mkdir -p $PROJECT_DIR/gene_filtering/11121/"

## Running Gene filtering [11121] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [11121] [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_11121 --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:v4 -c "sh -c 'python3 hvg_scanpy_opti.py  /data/asap2/users/1/xj31a6/cell_filtering/11098/output.loom /matrix /data/asap2/users/1/xj31a6/gene_filtering/11121 0.5 0.0125 3 Inf 20 None false 1> /data/asap2/users/1/xj31a6/gene_filtering/11121/exec.out 2> /data/asap2/users/1/xj31a6/gene_filtering/11121/exec.err'"


## ----------------------------------------------------------------
## Run 11122  Gene filtering  (Gene filtering #2 hvg)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/gene_filtering/11122/"

## Running Gene filtering [11122] [Gene filtering #2 hvg] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [11122] [Gene filtering #2 hvg] (input_matrix:cell_filtering #1)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_11122 --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:v4 -c "sh -c 'Rscript --vanilla filtering.R  /data/asap2/users/1/xj31a6/cell_filtering/11098/output.loom /data/asap2/users/1/xj31a6/gene_filtering/11122 hvg false 0.1 0.5 1> /data/asap2/users/1/xj31a6/gene_filtering/11122/exec.out 2> /data/asap2/users/1/xj31a6/gene_filtering/11122/exec.err'"


## ----------------------------------------------------------------
## Run 11123  Gene filtering  (Gene filtering #3 m3drop)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/gene_filtering/11123/"

## Running Gene filtering [11123] [Gene filtering #3 m3drop] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [11123] [Gene filtering #3 m3drop] (input_matrix:cell_filtering #1)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_11123 --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:v4 -c "sh -c 'Rscript --vanilla filtering.R  /data/asap2/users/1/xj31a6/cell_filtering/11098/output.loom /data/asap2/users/1/xj31a6/gene_filtering/11123 m3drop 0.05 1> /data/asap2/users/1/xj31a6/gene_filtering/11123/exec.out 2> /data/asap2/users/1/xj31a6/gene_filtering/11123/exec.err'"


## ----------------------------------------------------------------
## Run 13100  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:v4 -c "mkdir -p $PROJECT_DIR/normalization/13100/"

## Running Normalization [13100] [Normalization #1 asap_seurat] (input_matrix:cell_filtering #1)
echo '-> Running Normalization [13100] [Normalization #1 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_13100 --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:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Normalization -loom /data/asap2/users/1/xj31a6/cell_filtering/11098/output.loom -o /data/asap2/users/1/xj31a6/normalization/13100/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/xj31a6/normalization/13100/exec.out 2> /data/asap2/users/1/xj31a6/normalization/13100/exec.err'"


## ----------------------------------------------------------------
## Run 13101  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:v4 -c "mkdir -p $PROJECT_DIR/normalization/13101/"

## Running Normalization [13101] [Normalization #2 asap_seurat] (input_matrix:gene_filtering #1)
echo '-> Running Normalization [13101] [Normalization #2 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_13101 --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:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Normalization -loom /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom -o /data/asap2/users/1/xj31a6/normalization/13101/output.json -oAnnot /layers/norm_2_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/xj31a6/normalization/13101/exec.out 2> /data/asap2/users/1/xj31a6/normalization/13101/exec.err'"


## ----------------------------------------------------------------
## Run 13104  Gene filtering  (Gene filtering #4 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/gene_filtering/13104/"

## Running Gene filtering [13104] [Gene filtering #4 basic] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [13104] [Gene filtering #4 basic] (input_matrix:cell_filtering #1)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_13104 --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:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T FilterRows -loom /data/asap2/users/1/xj31a6/cell_filtering/11098/output.loom -o /data/asap2/users/1/xj31a6/gene_filtering/13104 -m basic  1> /data/asap2/users/1/xj31a6/gene_filtering/13104/exec.out 2> /data/asap2/users/1/xj31a6/gene_filtering/13104/exec.err'"


## ----------------------------------------------------------------
## Run 13105  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:v4 -c "mkdir -p $PROJECT_DIR/scaling/13105/"

## Running Scaling [13105] [Scaling #1 asap_seurat] (input_matrix:normalization #2)
echo '-> Running Scaling [13105] [Scaling #1 asap_seurat] (input_matrix:normalization #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_13105 --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:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Scaling -loom /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom -o /data/asap2/users/1/xj31a6/scaling/13105/output.json -iAnnot /layers/norm_2_asap_seurat -oAnnot /layers/scaling_1_asap_seurat -scale true -center true -scaleMax 10  1> /data/asap2/users/1/xj31a6/scaling/13105/exec.out 2> /data/asap2/users/1/xj31a6/scaling/13105/exec.err'"


## ----------------------------------------------------------------
## Run 13110  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:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/13110/"

## Running Dimension reduction [13110] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1)
echo '-> Running Dimension reduction [13110] [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_13110 --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:v4 -c "sh -c 'python3 pca_scanpy_opti.py  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /layers/scaling_1_asap_seurat /col_attrs/_dr_1_inc_pca_50D /data/asap2/users/1/xj31a6/dim_reduction/13110/output.json 50 10000 20 1> /data/asap2/users/1/xj31a6/dim_reduction/13110/exec.out 2> /data/asap2/users/1/xj31a6/dim_reduction/13110/exec.err'"


## ----------------------------------------------------------------
## Run 13116  Clustering  (Clustering #1 seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/clustering/13116/"

## Running Clustering [13116] [Clustering #1 seurat] (input_matrix:dim_reduction #1)
echo '-> Running Clustering [13116] [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_13116 --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:v4 -c "sh -c 'Rscript --vanilla clustering.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/clustering/13116 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_1_seurat 20 0.8 louvain 1> /data/asap2/users/1/xj31a6/clustering/13116/exec.out 2> /data/asap2/users/1/xj31a6/clustering/13116/exec.err'"


## ----------------------------------------------------------------
## Run 13133  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:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/13133/"

## Running Dimension reduction [13133] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 Number of dimensions:2 Min distance:0.05)
echo '-> Running Dimension reduction [13133] [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_13133 --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:v4 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/dim_reduction/13133 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_2_umap_2D 2 0.05 30 correlation 1> /data/asap2/users/1/xj31a6/dim_reduction/13133/exec.out 2> /data/asap2/users/1/xj31a6/dim_reduction/13133/exec.err'"


## ----------------------------------------------------------------
## Run 13134  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:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/13134/"

## Running Dimension reduction [13134] [Dimension reduction #3 umap] (input_matrix:dim_reduction #1 Number of dimensions:3 Min distance:0.05)
echo '-> Running Dimension reduction [13134] [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_13134 --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:v4 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/dim_reduction/13134 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_3_umap_3D 3 0.05 30 correlation 1> /data/asap2/users/1/xj31a6/dim_reduction/13134/exec.out 2> /data/asap2/users/1/xj31a6/dim_reduction/13134/exec.err'"


## ----------------------------------------------------------------
## Run 13136  Dimension reduction  (Dimension reduction #5 tsne)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/13136/"

## Running Dimension reduction [13136] [Dimension reduction #5 tsne] (input_matrix:dim_reduction #1 Number of dimensions:3 Perplexity:200 Theta:0)
echo '-> Running Dimension reduction [13136] [Dimension reduction #5 tsne] (input_matrix:dim_reduction #1 Number of dimensions:3 Perplexity:200 Theta: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_13136 --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:v4 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/dim_reduction/13136 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_5_tsne_3D 3 200 0 1> /data/asap2/users/1/xj31a6/dim_reduction/13136/exec.out 2> /data/asap2/users/1/xj31a6/dim_reduction/13136/exec.err'"


## ----------------------------------------------------------------
## Run 13296  Dimension reduction  (Dimension reduction #6 tsne)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/13296/"

## Running Dimension reduction [13296] [Dimension reduction #6 tsne] (input_matrix:dim_reduction #1 Number of dimensions:2 Perplexity:200 Theta:0)
echo '-> Running Dimension reduction [13296] [Dimension reduction #6 tsne] (input_matrix:dim_reduction #1 Number of dimensions:2 Perplexity:200 Theta: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_13296 --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:v4 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/dim_reduction/13296 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_6_tsne_2D 2 200 0 1> /data/asap2/users/1/xj31a6/dim_reduction/13296/exec.out 2> /data/asap2/users/1/xj31a6/dim_reduction/13296/exec.err'"


## ----------------------------------------------------------------
## Run 13563  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:v4 -c "mkdir -p $PROJECT_DIR/de/13563/"

## Running Differential expression [13563] [Differential expression #1 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:1 Compared group:)
echo '-> Running Differential expression [13563] [Differential expression #1 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 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_13563 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13563 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_1_wilcox-seurat null /col_attrs/_clust_1_seurat 1 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13563/exec.out 2> /data/asap2/users/1/xj31a6/de/13563/exec.err'"


## ----------------------------------------------------------------
## Run 13564  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:v4 -c "mkdir -p $PROJECT_DIR/de/13564/"

## Running Differential expression [13564] [Differential expression #2 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:2 Compared group:)
echo '-> Running Differential expression [13564] [Differential expression #2 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:2 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_13564 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13564 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_2_wilcox-seurat null /col_attrs/_clust_1_seurat 2 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13564/exec.out 2> /data/asap2/users/1/xj31a6/de/13564/exec.err'"


## ----------------------------------------------------------------
## Run 13565  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:v4 -c "mkdir -p $PROJECT_DIR/de/13565/"

## Running Differential expression [13565] [Differential expression #3 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:3 Compared group:)
echo '-> Running Differential expression [13565] [Differential expression #3 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:3 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_13565 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13565 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_3_wilcox-seurat null /col_attrs/_clust_1_seurat 3 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13565/exec.out 2> /data/asap2/users/1/xj31a6/de/13565/exec.err'"


## ----------------------------------------------------------------
## Run 13566  Differential expression  (Differential expression #4 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13566/"

## Running Differential expression [13566] [Differential expression #4 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:4 Compared group:)
echo '-> Running Differential expression [13566] [Differential expression #4 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:4 Compared group:)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_13566 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13566 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_4_wilcox-seurat null /col_attrs/_clust_1_seurat 4 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13566/exec.out 2> /data/asap2/users/1/xj31a6/de/13566/exec.err'"


## ----------------------------------------------------------------
## Run 13567  Differential expression  (Differential expression #5 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13567/"

## Running Differential expression [13567] [Differential expression #5 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:5 Compared group:)
echo '-> Running Differential expression [13567] [Differential expression #5 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:5 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_13567 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13567 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_5_wilcox-seurat null /col_attrs/_clust_1_seurat 5 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13567/exec.out 2> /data/asap2/users/1/xj31a6/de/13567/exec.err'"


## ----------------------------------------------------------------
## Run 13568  Differential expression  (Differential expression #6 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13568/"

## Running Differential expression [13568] [Differential expression #6 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:6 Compared group:)
echo '-> Running Differential expression [13568] [Differential expression #6 wilcox-seurat] (input_matrix:normalization #2 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_13568 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13568 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_6_wilcox-seurat null /col_attrs/_clust_1_seurat 6 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13568/exec.out 2> /data/asap2/users/1/xj31a6/de/13568/exec.err'"


## ----------------------------------------------------------------
## Run 13569  Differential expression  (Differential expression #7 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13569/"

## Running Differential expression [13569] [Differential expression #7 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:7 Compared group:)
echo '-> Running Differential expression [13569] [Differential expression #7 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:7 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_13569 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13569 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_7_wilcox-seurat null /col_attrs/_clust_1_seurat 7 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13569/exec.out 2> /data/asap2/users/1/xj31a6/de/13569/exec.err'"


## ----------------------------------------------------------------
## Run 13570  Differential expression  (Differential expression #8 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13570/"

## Running Differential expression [13570] [Differential expression #8 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:8 Compared group:)
echo '-> Running Differential expression [13570] [Differential expression #8 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:8 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_13570 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13570 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_8_wilcox-seurat null /col_attrs/_clust_1_seurat 8 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13570/exec.out 2> /data/asap2/users/1/xj31a6/de/13570/exec.err'"


## ----------------------------------------------------------------
## Run 13571  Differential expression  (Differential expression #9 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13571/"

## Running Differential expression [13571] [Differential expression #9 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:9 Compared group:)
echo '-> Running Differential expression [13571] [Differential expression #9 wilcox-seurat] (input_matrix:normalization #2 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_13571 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13571 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_9_wilcox-seurat null /col_attrs/_clust_1_seurat 9 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13571/exec.out 2> /data/asap2/users/1/xj31a6/de/13571/exec.err'"


## ----------------------------------------------------------------
## Run 13572  Differential expression  (Differential expression #10 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13572/"

## Running Differential expression [13572] [Differential expression #10 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:10 Compared group:)
echo '-> Running Differential expression [13572] [Differential expression #10 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:10 Compared group:)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_13572 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13572 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_10_wilcox-seurat null /col_attrs/_clust_1_seurat 10 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13572/exec.out 2> /data/asap2/users/1/xj31a6/de/13572/exec.err'"


## ----------------------------------------------------------------
## Run 13573  Differential expression  (Differential expression #11 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13573/"

## Running Differential expression [13573] [Differential expression #11 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:11 Compared group:)
echo '-> Running Differential expression [13573] [Differential expression #11 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:11 Compared group:)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_13573 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13573 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_11_wilcox-seurat null /col_attrs/_clust_1_seurat 11 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13573/exec.out 2> /data/asap2/users/1/xj31a6/de/13573/exec.err'"


## ----------------------------------------------------------------
## Run 13574  Differential expression  (Differential expression #12 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13574/"

## Running Differential expression [13574] [Differential expression #12 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:12 Compared group:)
echo '-> Running Differential expression [13574] [Differential expression #12 wilcox-seurat] (input_matrix:normalization #2 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_13574 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13574 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_12_wilcox-seurat null /col_attrs/_clust_1_seurat 12 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13574/exec.out 2> /data/asap2/users/1/xj31a6/de/13574/exec.err'"


## ----------------------------------------------------------------
## Run 13575  Differential expression  (Differential expression #13 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13575/"

## Running Differential expression [13575] [Differential expression #13 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:13 Compared group:)
echo '-> Running Differential expression [13575] [Differential expression #13 wilcox-seurat] (input_matrix:normalization #2 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_13575 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13575 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_13_wilcox-seurat null /col_attrs/_clust_1_seurat 13 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13575/exec.out 2> /data/asap2/users/1/xj31a6/de/13575/exec.err'"


## ----------------------------------------------------------------
## Run 13576  Differential expression  (Differential expression #14 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13576/"

## Running Differential expression [13576] [Differential expression #14 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:14 Compared group:)
echo '-> Running Differential expression [13576] [Differential expression #14 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:14 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_13576 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13576 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_14_wilcox-seurat null /col_attrs/_clust_1_seurat 14 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13576/exec.out 2> /data/asap2/users/1/xj31a6/de/13576/exec.err'"


## ----------------------------------------------------------------
## Run 13577  Differential expression  (Differential expression #15 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13577/"

## Running Differential expression [13577] [Differential expression #15 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:15 Compared group:)
echo '-> Running Differential expression [13577] [Differential expression #15 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:15 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_13577 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13577 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_15_wilcox-seurat null /col_attrs/_clust_1_seurat 15 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13577/exec.out 2> /data/asap2/users/1/xj31a6/de/13577/exec.err'"


## ----------------------------------------------------------------
## Run 13578  Differential expression  (Differential expression #16 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13578/"

## Running Differential expression [13578] [Differential expression #16 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:16 Compared group:)
echo '-> Running Differential expression [13578] [Differential expression #16 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:16 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_13578 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13578 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_16_wilcox-seurat null /col_attrs/_clust_1_seurat 16 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13578/exec.out 2> /data/asap2/users/1/xj31a6/de/13578/exec.err'"


## ----------------------------------------------------------------
## Run 13579  Differential expression  (Differential expression #17 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13579/"

## Running Differential expression [13579] [Differential expression #17 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:17 Compared group:)
echo '-> Running Differential expression [13579] [Differential expression #17 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:17 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_13579 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13579 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_17_wilcox-seurat null /col_attrs/_clust_1_seurat 17 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13579/exec.out 2> /data/asap2/users/1/xj31a6/de/13579/exec.err'"


## ----------------------------------------------------------------
## Run 13580  Differential expression  (Differential expression #18 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13580/"

## Running Differential expression [13580] [Differential expression #18 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:18 Compared group:)
echo '-> Running Differential expression [13580] [Differential expression #18 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:18 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_13580 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13580 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_18_wilcox-seurat null /col_attrs/_clust_1_seurat 18 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13580/exec.out 2> /data/asap2/users/1/xj31a6/de/13580/exec.err'"


## ----------------------------------------------------------------
## Run 13581  Differential expression  (Differential expression #19 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13581/"

## Running Differential expression [13581] [Differential expression #19 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:19 Compared group:)
echo '-> Running Differential expression [13581] [Differential expression #19 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:19 Compared group:)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_13581 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13581 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_19_wilcox-seurat null /col_attrs/_clust_1_seurat 19 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13581/exec.out 2> /data/asap2/users/1/xj31a6/de/13581/exec.err'"


## ----------------------------------------------------------------
## Run 13582  Differential expression  (Differential expression #20 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13582/"

## Running Differential expression [13582] [Differential expression #20 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:20 Compared group:)
echo '-> Running Differential expression [13582] [Differential expression #20 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:20 Compared group:)'

## Command
docker run -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --name asap_dev_13582 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13582 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_20_wilcox-seurat null /col_attrs/_clust_1_seurat 20 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13582/exec.out 2> /data/asap2/users/1/xj31a6/de/13582/exec.err'"


## ----------------------------------------------------------------
## Run 13583  Differential expression  (Differential expression #21 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13583/"

## Running Differential expression [13583] [Differential expression #21 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:21 Compared group:)
echo '-> Running Differential expression [13583] [Differential expression #21 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:21 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_13583 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13583 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_21_wilcox-seurat null /col_attrs/_clust_1_seurat 21 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13583/exec.out 2> /data/asap2/users/1/xj31a6/de/13583/exec.err'"


## ----------------------------------------------------------------
## Run 13584  Differential expression  (Differential expression #22 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13584/"

## Running Differential expression [13584] [Differential expression #22 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:22 Compared group:)
echo '-> Running Differential expression [13584] [Differential expression #22 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:22 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_13584 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13584 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_22_wilcox-seurat null /col_attrs/_clust_1_seurat 22 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13584/exec.out 2> /data/asap2/users/1/xj31a6/de/13584/exec.err'"


## ----------------------------------------------------------------
## Run 13585  Differential expression  (Differential expression #23 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13585/"

## Running Differential expression [13585] [Differential expression #23 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:23 Compared group:)
echo '-> Running Differential expression [13585] [Differential expression #23 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:23 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_13585 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13585 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_23_wilcox-seurat null /col_attrs/_clust_1_seurat 23 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13585/exec.out 2> /data/asap2/users/1/xj31a6/de/13585/exec.err'"


## ----------------------------------------------------------------
## Run 13586  Differential expression  (Differential expression #24 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13586/"

## Running Differential expression [13586] [Differential expression #24 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:24 Compared group:)
echo '-> Running Differential expression [13586] [Differential expression #24 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:24 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_13586 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13586 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_24_wilcox-seurat null /col_attrs/_clust_1_seurat 24 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13586/exec.out 2> /data/asap2/users/1/xj31a6/de/13586/exec.err'"


## ----------------------------------------------------------------
## Run 13587  Differential expression  (Differential expression #25 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13587/"

## Running Differential expression [13587] [Differential expression #25 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:25 Compared group:)
echo '-> Running Differential expression [13587] [Differential expression #25 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:25 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_13587 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13587 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_25_wilcox-seurat null /col_attrs/_clust_1_seurat 25 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13587/exec.out 2> /data/asap2/users/1/xj31a6/de/13587/exec.err'"


## ----------------------------------------------------------------
## Run 13588  Differential expression  (Differential expression #26 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13588/"

## Running Differential expression [13588] [Differential expression #26 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:26 Compared group:)
echo '-> Running Differential expression [13588] [Differential expression #26 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:26 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_13588 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13588 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_26_wilcox-seurat null /col_attrs/_clust_1_seurat 26 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13588/exec.out 2> /data/asap2/users/1/xj31a6/de/13588/exec.err'"


## ----------------------------------------------------------------
## Run 13589  Differential expression  (Differential expression #27 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13589/"

## Running Differential expression [13589] [Differential expression #27 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:27 Compared group:)
echo '-> Running Differential expression [13589] [Differential expression #27 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:27 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_13589 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13589 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_27_wilcox-seurat null /col_attrs/_clust_1_seurat 27 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13589/exec.out 2> /data/asap2/users/1/xj31a6/de/13589/exec.err'"


## ----------------------------------------------------------------
## Run 13590  Differential expression  (Differential expression #28 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13590/"

## Running Differential expression [13590] [Differential expression #28 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:28 Compared group:)
echo '-> Running Differential expression [13590] [Differential expression #28 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:28 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_13590 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13590 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_28_wilcox-seurat null /col_attrs/_clust_1_seurat 28 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13590/exec.out 2> /data/asap2/users/1/xj31a6/de/13590/exec.err'"


## ----------------------------------------------------------------
## Run 13591  Differential expression  (Differential expression #29 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13591/"

## Running Differential expression [13591] [Differential expression #29 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:29 Compared group:)
echo '-> Running Differential expression [13591] [Differential expression #29 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:29 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_13591 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13591 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_29_wilcox-seurat null /col_attrs/_clust_1_seurat 29 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13591/exec.out 2> /data/asap2/users/1/xj31a6/de/13591/exec.err'"


## ----------------------------------------------------------------
## Run 13592  Differential expression  (Differential expression #30 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13592/"

## Running Differential expression [13592] [Differential expression #30 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:30 Compared group:)
echo '-> Running Differential expression [13592] [Differential expression #30 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:30 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_13592 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13592 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_30_wilcox-seurat null /col_attrs/_clust_1_seurat 30 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13592/exec.out 2> /data/asap2/users/1/xj31a6/de/13592/exec.err'"


## ----------------------------------------------------------------
## Run 13593  Differential expression  (Differential expression #31 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13593/"

## Running Differential expression [13593] [Differential expression #31 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:31 Compared group:)
echo '-> Running Differential expression [13593] [Differential expression #31 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:31 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_13593 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13593 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_31_wilcox-seurat null /col_attrs/_clust_1_seurat 31 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13593/exec.out 2> /data/asap2/users/1/xj31a6/de/13593/exec.err'"


## ----------------------------------------------------------------
## Run 13594  Differential expression  (Differential expression #32 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13594/"

## Running Differential expression [13594] [Differential expression #32 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:32 Compared group:)
echo '-> Running Differential expression [13594] [Differential expression #32 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:32 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_13594 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13594 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_32_wilcox-seurat null /col_attrs/_clust_1_seurat 32 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13594/exec.out 2> /data/asap2/users/1/xj31a6/de/13594/exec.err'"


## ----------------------------------------------------------------
## Run 13595  Differential expression  (Differential expression #33 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13595/"

## Running Differential expression [13595] [Differential expression #33 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:33 Compared group:)
echo '-> Running Differential expression [13595] [Differential expression #33 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:33 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_13595 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13595 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_33_wilcox-seurat null /col_attrs/_clust_1_seurat 33 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13595/exec.out 2> /data/asap2/users/1/xj31a6/de/13595/exec.err'"


## ----------------------------------------------------------------
## Run 13596  Differential expression  (Differential expression #34 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13596/"

## Running Differential expression [13596] [Differential expression #34 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:34 Compared group:)
echo '-> Running Differential expression [13596] [Differential expression #34 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:34 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_13596 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13596 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_34_wilcox-seurat null /col_attrs/_clust_1_seurat 34 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13596/exec.out 2> /data/asap2/users/1/xj31a6/de/13596/exec.err'"


## ----------------------------------------------------------------
## Run 13597  Differential expression  (Differential expression #35 wilcox-seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/13597/"

## Running Differential expression [13597] [Differential expression #35 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:35 Compared group:)
echo '-> Running Differential expression [13597] [Differential expression #35 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 Reference group:35 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_13597 --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:v4 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13597 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_35_wilcox-seurat null /col_attrs/_clust_1_seurat 35 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13597/exec.out 2> /data/asap2/users/1/xj31a6/de/13597/exec.err'"


## ----------------------------------------------------------------
## Run 784310  Find markers  (Find markers #1 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/markers/784310/"

## Running Find markers [784310] [Find markers #1 asap_markers] (input_matrix:gene_filtering #1)
echo '-> Running Find markers [784310] [Find markers #1 asap_markers] (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_784310 --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:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/xj31a6/gene_filtering/11121/output.loom -o /data/asap2/users/1/xj31a6/markers/784310 --iAnnot /col_attrs/_clust_1_seurat --id 47889 --is_count_table true  1> /data/asap2/users/1/xj31a6/markers/784310/exec.out 2> /data/asap2/users/1/xj31a6/markers/784310/exec.err'"