## This script contains all commands executed in the PROJECT xr7ne3 and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT xr7ne3 / ASAP4**********************'
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/xr7ne3
## 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/marker_enrich/ && 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/xr7ne3/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 11099  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/11099/"

## writing file $PROJECT_DIR/cell_filtering/11099/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/11099/discarded_cols.json'
## writing file $PROJECT_DIR/cell_filtering/11099/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/11099/manually_discarded_cols.json'
## Running Cell filtering [11099] [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 [11099] [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/asap2_test:/data/asap2_test --name asap_dev_11099 --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/xr7ne3/parsing/output.loom -o /data/asap2/users/1/xr7ne3/cell_filtering/11099 -col_indexes_file /data/asap2/users/1/xr7ne3/cell_filtering/11099/discarded_cols.json  1> /data/asap2/users/1/xr7ne3/cell_filtering/11099/exec.out 2> /data/asap2/users/1/xr7ne3/cell_filtering/11099/exec.err'"


## ----------------------------------------------------------------
## Run 11118  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/11118/"

## Running Gene filtering [11118] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [11118] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11118 --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/xr7ne3/cell_filtering/11099/output.loom /matrix /data/asap2/users/1/xr7ne3/gene_filtering/11118 0.5 0.0125 3 Inf 20 None false 1> /data/asap2/users/1/xr7ne3/gene_filtering/11118/exec.out 2> /data/asap2/users/1/xr7ne3/gene_filtering/11118/exec.err'"


## ----------------------------------------------------------------
## Run 11119  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/11119/"

## Running Gene filtering [11119] [Gene filtering #2 hvg] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [11119] [Gene filtering #2 hvg] (input_matrix:cell_filtering #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11119 --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/xr7ne3/cell_filtering/11099/output.loom /data/asap2/users/1/xr7ne3/gene_filtering/11119 hvg false 0.1 0.5 1> /data/asap2/users/1/xr7ne3/gene_filtering/11119/exec.out 2> /data/asap2/users/1/xr7ne3/gene_filtering/11119/exec.err'"


## ----------------------------------------------------------------
## Run 11120  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/11120/"

## Running Gene filtering [11120] [Gene filtering #3 m3drop] (input_matrix:cell_filtering #1)
echo '-> Running Gene filtering [11120] [Gene filtering #3 m3drop] (input_matrix:cell_filtering #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11120 --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/xr7ne3/cell_filtering/11099/output.loom /data/asap2/users/1/xr7ne3/gene_filtering/11120 m3drop 0.05 1> /data/asap2/users/1/xr7ne3/gene_filtering/11120/exec.out 2> /data/asap2/users/1/xr7ne3/gene_filtering/11120/exec.err'"


## ----------------------------------------------------------------
## Run 13081  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/13081/"

## Running Normalization [13081] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1)
echo '-> Running Normalization [13081] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13081 --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/xr7ne3/gene_filtering/11118/output.loom -o /data/asap2/users/1/xr7ne3/normalization/13081/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/xr7ne3/normalization/13081/exec.out 2> /data/asap2/users/1/xr7ne3/normalization/13081/exec.err'"


## ----------------------------------------------------------------
## Run 13083  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/13083/"

## Running Scaling [13083] [Scaling #1 asap_seurat] (input_matrix:normalization #1)
echo '-> Running Scaling [13083] [Scaling #1 asap_seurat] (input_matrix:normalization #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13083 --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/xr7ne3/gene_filtering/11118/output.loom -o /data/asap2/users/1/xr7ne3/scaling/13083/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/xr7ne3/scaling/13083/exec.out 2> /data/asap2/users/1/xr7ne3/scaling/13083/exec.err'"


## ----------------------------------------------------------------
## Run 13084  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/13084/"

## Running Normalization [13084] [Normalization #2 asap_seurat] (input_matrix:cell_filtering #1)
echo '-> Running Normalization [13084] [Normalization #2 asap_seurat] (input_matrix:cell_filtering #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13084 --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/xr7ne3/cell_filtering/11099/output.loom -o /data/asap2/users/1/xr7ne3/normalization/13084/output.json -oAnnot /layers/norm_2_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/xr7ne3/normalization/13084/exec.out 2> /data/asap2/users/1/xr7ne3/normalization/13084/exec.err'"


## ----------------------------------------------------------------
## Run 13085  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/13085/"

## Running Dimension reduction [13085] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1)
echo '-> Running Dimension reduction [13085] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13085 --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/xr7ne3/gene_filtering/11118/output.loom /layers/scaling_1_asap_seurat /col_attrs/_dr_1_inc_pca_50D /data/asap2/users/1/xr7ne3/dim_reduction/13085/output.json 50 10000 20 1> /data/asap2/users/1/xr7ne3/dim_reduction/13085/exec.out 2> /data/asap2/users/1/xr7ne3/dim_reduction/13085/exec.err'"


## ----------------------------------------------------------------
## Run 13219  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/13219/"

## Running Clustering [13219] [Clustering #1 seurat] (input_matrix:dim_reduction #1)
echo '-> Running Clustering [13219] [Clustering #1 seurat] (input_matrix:dim_reduction #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13219 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/clustering/13219 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_1_seurat 20 0.8 louvain 1> /data/asap2/users/1/xr7ne3/clustering/13219/exec.out 2> /data/asap2/users/1/xr7ne3/clustering/13219/exec.err'"


## ----------------------------------------------------------------
## Run 13225  Dimension reduction  (Dimension reduction #8 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/13225/"

## Running Dimension reduction [13225] [Dimension reduction #8 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.05)
echo '-> Running Dimension reduction [13225] [Dimension reduction #8 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.05)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13225 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/dim_reduction/13225 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_8_umap_2D 2 0.05 30 correlation 1> /data/asap2/users/1/xr7ne3/dim_reduction/13225/exec.out 2> /data/asap2/users/1/xr7ne3/dim_reduction/13225/exec.err'"


## ----------------------------------------------------------------
## Run 13226  Dimension reduction  (Dimension reduction #9 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/13226/"

## Running Dimension reduction [13226] [Dimension reduction #9 umap] (input_matrix:dim_reduction #1 nber_dims:3 min_dist:0.05)
echo '-> Running Dimension reduction [13226] [Dimension reduction #9 umap] (input_matrix:dim_reduction #1 nber_dims:3 min_dist:0.05)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13226 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/dim_reduction/13226 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_9_umap_3D 3 0.05 30 correlation 1> /data/asap2/users/1/xr7ne3/dim_reduction/13226/exec.out 2> /data/asap2/users/1/xr7ne3/dim_reduction/13226/exec.err'"


## ----------------------------------------------------------------
## Run 13420  Dimension reduction  (Dimension reduction #10 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/13420/"

## Running Dimension reduction [13420] [Dimension reduction #10 tsne] (input_matrix:dim_reduction #1 nber_dims:2 perplexity:200 theta:0)
echo '-> Running Dimension reduction [13420] [Dimension reduction #10 tsne] (input_matrix:dim_reduction #1 nber_dims:2 perplexity:200 theta:0)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13420 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/dim_reduction/13420 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_10_tsne_2D 2 200 0 1> /data/asap2/users/1/xr7ne3/dim_reduction/13420/exec.out 2> /data/asap2/users/1/xr7ne3/dim_reduction/13420/exec.err'"


## ----------------------------------------------------------------
## Run 13421  Dimension reduction  (Dimension reduction #11 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/13421/"

## Running Dimension reduction [13421] [Dimension reduction #11 tsne] (input_matrix:dim_reduction #1 nber_dims:3 perplexity:200 theta:0)
echo '-> Running Dimension reduction [13421] [Dimension reduction #11 tsne] (input_matrix:dim_reduction #1 nber_dims:3 perplexity:200 theta:0)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13421 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/dim_reduction/13421 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_11_tsne_3D 3 200 0 1> /data/asap2/users/1/xr7ne3/dim_reduction/13421/exec.out 2> /data/asap2/users/1/xr7ne3/dim_reduction/13421/exec.err'"


## ----------------------------------------------------------------
## Run 13813  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/13813/"

## Running Differential expression [13813] [Differential expression #1 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:1 group_comp:)
echo '-> Running Differential expression [13813] [Differential expression #1 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:1 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13813 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13813 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13813/exec.out 2> /data/asap2/users/1/xr7ne3/de/13813/exec.err'"


## ----------------------------------------------------------------
## Run 13814  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/13814/"

## Running Differential expression [13814] [Differential expression #2 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:2 group_comp:)
echo '-> Running Differential expression [13814] [Differential expression #2 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:2 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13814 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13814 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13814/exec.out 2> /data/asap2/users/1/xr7ne3/de/13814/exec.err'"


## ----------------------------------------------------------------
## Run 13815  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/13815/"

## Running Differential expression [13815] [Differential expression #3 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:3 group_comp:)
echo '-> Running Differential expression [13815] [Differential expression #3 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:3 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13815 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13815 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13815/exec.out 2> /data/asap2/users/1/xr7ne3/de/13815/exec.err'"


## ----------------------------------------------------------------
## Run 13816  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/13816/"

## Running Differential expression [13816] [Differential expression #4 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:4 group_comp:)
echo '-> Running Differential expression [13816] [Differential expression #4 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:4 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13816 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13816 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13816/exec.out 2> /data/asap2/users/1/xr7ne3/de/13816/exec.err'"


## ----------------------------------------------------------------
## Run 13817  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/13817/"

## Running Differential expression [13817] [Differential expression #5 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:5 group_comp:)
echo '-> Running Differential expression [13817] [Differential expression #5 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:5 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13817 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13817 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13817/exec.out 2> /data/asap2/users/1/xr7ne3/de/13817/exec.err'"


## ----------------------------------------------------------------
## Run 13818  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/13818/"

## Running Differential expression [13818] [Differential expression #6 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:6 group_comp:)
echo '-> Running Differential expression [13818] [Differential expression #6 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:6 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13818 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13818 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13818/exec.out 2> /data/asap2/users/1/xr7ne3/de/13818/exec.err'"


## ----------------------------------------------------------------
## Run 13819  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/13819/"

## Running Differential expression [13819] [Differential expression #7 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:7 group_comp:)
echo '-> Running Differential expression [13819] [Differential expression #7 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:7 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13819 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13819 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13819/exec.out 2> /data/asap2/users/1/xr7ne3/de/13819/exec.err'"


## ----------------------------------------------------------------
## Run 13820  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/13820/"

## Running Differential expression [13820] [Differential expression #8 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:8 group_comp:)
echo '-> Running Differential expression [13820] [Differential expression #8 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:8 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13820 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13820 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13820/exec.out 2> /data/asap2/users/1/xr7ne3/de/13820/exec.err'"


## ----------------------------------------------------------------
## Run 13821  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/13821/"

## Running Differential expression [13821] [Differential expression #9 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:9 group_comp:)
echo '-> Running Differential expression [13821] [Differential expression #9 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:9 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13821 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13821 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13821/exec.out 2> /data/asap2/users/1/xr7ne3/de/13821/exec.err'"


## ----------------------------------------------------------------
## Run 13822  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/13822/"

## Running Differential expression [13822] [Differential expression #10 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:10 group_comp:)
echo '-> Running Differential expression [13822] [Differential expression #10 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:10 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13822 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13822 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13822/exec.out 2> /data/asap2/users/1/xr7ne3/de/13822/exec.err'"


## ----------------------------------------------------------------
## Run 13823  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/13823/"

## Running Differential expression [13823] [Differential expression #11 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:11 group_comp:)
echo '-> Running Differential expression [13823] [Differential expression #11 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:11 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13823 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13823 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13823/exec.out 2> /data/asap2/users/1/xr7ne3/de/13823/exec.err'"


## ----------------------------------------------------------------
## Run 13824  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/13824/"

## Running Differential expression [13824] [Differential expression #12 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:12 group_comp:)
echo '-> Running Differential expression [13824] [Differential expression #12 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:12 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13824 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13824 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13824/exec.out 2> /data/asap2/users/1/xr7ne3/de/13824/exec.err'"


## ----------------------------------------------------------------
## Run 13825  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/13825/"

## Running Differential expression [13825] [Differential expression #13 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:13 group_comp:)
echo '-> Running Differential expression [13825] [Differential expression #13 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:13 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13825 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13825 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13825/exec.out 2> /data/asap2/users/1/xr7ne3/de/13825/exec.err'"


## ----------------------------------------------------------------
## Run 13826  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/13826/"

## Running Differential expression [13826] [Differential expression #14 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:14 group_comp:)
echo '-> Running Differential expression [13826] [Differential expression #14 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:14 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13826 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13826 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13826/exec.out 2> /data/asap2/users/1/xr7ne3/de/13826/exec.err'"


## ----------------------------------------------------------------
## Run 13827  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/13827/"

## Running Differential expression [13827] [Differential expression #15 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:15 group_comp:)
echo '-> Running Differential expression [13827] [Differential expression #15 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:15 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13827 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13827 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13827/exec.out 2> /data/asap2/users/1/xr7ne3/de/13827/exec.err'"


## ----------------------------------------------------------------
## Run 13828  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/13828/"

## Running Differential expression [13828] [Differential expression #16 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:16 group_comp:)
echo '-> Running Differential expression [13828] [Differential expression #16 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:16 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13828 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13828 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13828/exec.out 2> /data/asap2/users/1/xr7ne3/de/13828/exec.err'"


## ----------------------------------------------------------------
## Run 13829  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/13829/"

## Running Differential expression [13829] [Differential expression #17 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:17 group_comp:)
echo '-> Running Differential expression [13829] [Differential expression #17 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:17 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13829 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13829 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13829/exec.out 2> /data/asap2/users/1/xr7ne3/de/13829/exec.err'"


## ----------------------------------------------------------------
## Run 13830  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/13830/"

## Running Differential expression [13830] [Differential expression #18 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:18 group_comp:)
echo '-> Running Differential expression [13830] [Differential expression #18 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:18 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13830 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13830 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13830/exec.out 2> /data/asap2/users/1/xr7ne3/de/13830/exec.err'"


## ----------------------------------------------------------------
## Run 13831  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/13831/"

## Running Differential expression [13831] [Differential expression #19 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:19 group_comp:)
echo '-> Running Differential expression [13831] [Differential expression #19 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:19 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13831 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13831 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13831/exec.out 2> /data/asap2/users/1/xr7ne3/de/13831/exec.err'"


## ----------------------------------------------------------------
## Run 13832  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/13832/"

## Running Differential expression [13832] [Differential expression #20 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:20 group_comp:)
echo '-> Running Differential expression [13832] [Differential expression #20 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:20 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13832 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13832 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13832/exec.out 2> /data/asap2/users/1/xr7ne3/de/13832/exec.err'"


## ----------------------------------------------------------------
## Run 13833  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/13833/"

## Running Differential expression [13833] [Differential expression #21 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:21 group_comp:)
echo '-> Running Differential expression [13833] [Differential expression #21 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:21 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13833 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13833 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13833/exec.out 2> /data/asap2/users/1/xr7ne3/de/13833/exec.err'"


## ----------------------------------------------------------------
## Run 13834  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/13834/"

## Running Differential expression [13834] [Differential expression #22 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:22 group_comp:)
echo '-> Running Differential expression [13834] [Differential expression #22 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:22 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13834 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13834 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13834/exec.out 2> /data/asap2/users/1/xr7ne3/de/13834/exec.err'"


## ----------------------------------------------------------------
## Run 13835  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/13835/"

## Running Differential expression [13835] [Differential expression #23 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:23 group_comp:)
echo '-> Running Differential expression [13835] [Differential expression #23 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:23 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13835 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13835 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13835/exec.out 2> /data/asap2/users/1/xr7ne3/de/13835/exec.err'"


## ----------------------------------------------------------------
## Run 13836  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/13836/"

## Running Differential expression [13836] [Differential expression #24 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:24 group_comp:)
echo '-> Running Differential expression [13836] [Differential expression #24 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:24 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13836 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13836 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13836/exec.out 2> /data/asap2/users/1/xr7ne3/de/13836/exec.err'"


## ----------------------------------------------------------------
## Run 13837  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/13837/"

## Running Differential expression [13837] [Differential expression #25 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:25 group_comp:)
echo '-> Running Differential expression [13837] [Differential expression #25 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:25 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13837 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13837 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13837/exec.out 2> /data/asap2/users/1/xr7ne3/de/13837/exec.err'"


## ----------------------------------------------------------------
## Run 13838  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/13838/"

## Running Differential expression [13838] [Differential expression #26 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:26 group_comp:)
echo '-> Running Differential expression [13838] [Differential expression #26 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:26 group_comp:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13838 --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/xr7ne3/gene_filtering/11118/output.loom /data/asap2/users/1/xr7ne3/de/13838 wilcox-seurat /layers/norm_1_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/xr7ne3/de/13838/exec.out 2> /data/asap2/users/1/xr7ne3/de/13838/exec.err'"


## ----------------------------------------------------------------
## Run 210432  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/210432/"

## Running Find markers [210432] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [210432] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_210432 --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/xr7ne3/gene_filtering/11118/output.loom -o /data/asap2/users/1/xr7ne3/markers/210432 --iAnnot /col_attrs/_clust_1_seurat --id 48116  1> /data/asap2/users/1/xr7ne3/markers/210432/exec.out 2> /data/asap2/users/1/xr7ne3/markers/210432/exec.err'"


## ----------------------------------------------------------------
## Run 210433  Marker enrichment  (Marker enrichment #2 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/marker_enrich/210433/"

## Running Marker enrichment [210433] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [210433] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_210433 --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 MarkerEnrichment -i /data/asap2/users/1/xr7ne3/markers/210432 -o /data/asap2/users/1/xr7ne3/markers/210433 --genesets 54,52,55,53,1720,1719,51,2761,50 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/xr7ne3/markers/210433/exec.out 2> /data/asap2/users/1/xr7ne3/markers/210433/exec.err'"


## ----------------------------------------------------------------
## Run 348099  Find markers  (Find markers #2 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/markers/348099/"

## Running Find markers [348099] [Find markers #2 asap_markers] (input_matrix:gene_filtering #1)
echo '-> Running Find markers [348099] [Find markers #2 asap_markers] (input_matrix:gene_filtering #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_348099 --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/xr7ne3/gene_filtering/11118/output.loom -o /data/asap2/users/1/xr7ne3/markers/348099 --iAnnot /col_attrs/_clust_1_seurat --id 48116 --is_count_table true  1> /data/asap2/users/1/xr7ne3/markers/348099/exec.out 2> /data/asap2/users/1/xr7ne3/markers/348099/exec.err'"


## ----------------------------------------------------------------
## Run 348100  Marker enrichment  (Marker enrichment #3 asap_marker_enrichment)
## ----------------------------------------------------------------

## 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/marker_enrich/348100/"

## Running Marker enrichment [348100] [Marker enrichment #3 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [348100] [Marker enrichment #3 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_348100 --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 MarkerEnrichment -i /data/asap2/users/1/xr7ne3/markers/348099 -o /data/asap2/users/1/xr7ne3/markers/348100 --genesets 54,52,55,53,1720,1719,51,2761,50 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/xr7ne3/markers/348100/exec.out 2> /data/asap2/users/1/xr7ne3/markers/348100/exec.err'"