## This script contains all commands executed in the PROJECT o8vex4 and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT o8vex4 / ASAP20**********************'
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/o8vex4
## Pull Docker images (must run before any docker run in this script)

docker pull fabdavid/asap_run:v5

## Host LOOM staging directory (inside Docker volume)
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $LOOM_DIR; chmod 777 $LOOM_DIR"

echo 'This project is PUBLIC => Nothing to do'

## Local PostgreSQL: create ASAP data database and load dump if missing
if ! psql -lqt | cut -d \| -f 1 | grep -qw asap_data_v5; then echo 'Create database asap_data_v5'; echo '$PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v5'; $PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v5; echo 'wget -qO - https://asap.epfl.ch/dumps/asap_data_v5.sql.gz | gunzip | grep -v \'AS integer\' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v5'; wget -qO - https://asap.epfl.ch/dumps/asap_data_v5.sql.gz | gunzip | grep -v 'AS integer' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v5; fi

## Project directory on the shared volume
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR"

## Step output directories (one folder per pipeline step that has runs)
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/parsing/ && mkdir -p $PROJECT_DIR/gene_filtering/ && mkdir -p $PROJECT_DIR/normalization/ && mkdir -p $PROJECT_DIR/dim_reduction/ && mkdir -p $PROJECT_DIR/clustering/ && mkdir -p $PROJECT_DIR/de/ && mkdir -p $PROJECT_DIR/ge/ && mkdir -p $PROJECT_DIR/cell_filtering/ && mkdir -p $PROJECT_DIR/removing_covariates/ && mkdir -p $PROJECT_DIR/cell_selection/ && mkdir -p $PROJECT_DIR/scaling/ && mkdir -p $PROJECT_DIR/module_score/"

## Parsed LOOM file (public: wget; private: place file then symlink as below)
echo 'Loading parsed Loom file...'
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "wget -qO $PROJECT_DIR/parsing/output.loom 'https://asap.epfl.ch/projects/o8vex4/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 47402  Cell filtering  (Cell filtering #1 qc_plots)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/cell_filtering/47402/"

## writing file $PROJECT_DIR/cell_filtering/47402/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/47402/discarded_cols.json'
docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "echo '{"discarded_cols":[143,591,14,71,87,95,109,161,164,172,210,214,225,226,258,267,278,281,303,335,347,434,448,494,501,506,532,538,10,13,20,32,54,57,58,61,62,67,73,80,89,112,119,135,141,156,160,165,187,188,191,200,242,250,251,265,269,289,293,309,310,312,313,322,326,331,348,369,393,394,421,424,425,426,429,430,432,438,454,459,461,465,479,507,511,543,554,558,566,578,579,582,600,606,615,622,626,628,637,663,665,24,39,42,97,108,305,371,384,388,440,452,456,539,548,648,658]}' > $PROJECT_DIR/cell_filtering/47402/discarded_cols.json"

## writing file $PROJECT_DIR/cell_filtering/47402/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/47402/manually_discarded_cols.json'
docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "echo '{"manually_discarded_cols":[]}' > $PROJECT_DIR/cell_filtering/47402/manually_discarded_cols.json"

## Running Cell filtering [47402] [Cell filtering #1 qc_plots] (manual_selection: depth:1000 detected_genes:1000 mito_content:20 protein_coding_content:80 ribo_content:2 nber_manually_discarded_cols:0 input_matrix:parsing)
echo '-> Running Cell filtering [47402] [Cell filtering #1 qc_plots] (manual_selection: depth:1000 detected_genes:1000 mito_content:20 protein_coding_content:80 ribo_content:2 nber_manually_discarded_cols:0 input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47402 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FilterCols -loom /data/asap2/users/462/o8vex4/parsing/output.loom -o /data/asap2/users/462/o8vex4/cell_filtering/32963 -col_indexes_file /data/asap2/users/462/o8vex4/cell_filtering/47402/discarded_cols.json  1> /data/asap2/users/462/o8vex4/cell_filtering/47402/exec.out 2> /data/asap2/users/462/o8vex4/cell_filtering/47402/exec.err'"


## ----------------------------------------------------------------
## Run 47403  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:v5 -c "mkdir -p $PROJECT_DIR/gene_filtering/47403/"

## Running Gene filtering [47403] [Gene filtering #2 hvg] (input_matrix:cell_filtering #1 fdr:0.1 min_disp:0.5)
echo '-> Running Gene filtering [47403] [Gene filtering #2 hvg] (input_matrix:cell_filtering #1 fdr:0.1 min_disp:0.5)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47403 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla filtering.R  /data/asap2/users/462/o8vex4/cell_filtering/47402/output.loom /matrix /data/asap2/users/462/o8vex4/gene_filtering/32966 hvg false 0.1 0.5 1> /data/asap2/users/462/o8vex4/gene_filtering/47403/exec.out 2> /data/asap2/users/462/o8vex4/gene_filtering/47403/exec.err'"


## ----------------------------------------------------------------
## Run 47404  Gene filtering  (Gene filtering #3 hvg_scanpy)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/gene_filtering/47404/"

## Running Gene filtering [47404] [Gene filtering #3 hvg_scanpy] (input_matrix:cell_filtering #1 n_bins:20 n_top_genes:3000 is_logged:false min_disp:0.5 max_disp:Inf min_mean:0.0125 max_mean:3)
echo '-> Running Gene filtering [47404] [Gene filtering #3 hvg_scanpy] (input_matrix:cell_filtering #1 n_bins:20 n_top_genes:3000 is_logged:false min_disp:0.5 max_disp:Inf min_mean:0.0125 max_mean:3)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47404 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'python3 hvg_scanpy_opti.py  /data/asap2/users/462/o8vex4/cell_filtering/47402/output.loom /matrix /data/asap2/users/462/o8vex4/gene_filtering/32967 0.5 0.0125 3 Inf 20 3000 false 1> /data/asap2/users/462/o8vex4/gene_filtering/47404/exec.out 2> /data/asap2/users/462/o8vex4/gene_filtering/47404/exec.err'"


## ----------------------------------------------------------------
## Run 47405  Normalization  (Normalization #1 asap_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/normalization/47405/"

## Running Normalization [47405] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #2 scale_factor:10000)
echo '-> Running Normalization [47405] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #2 scale_factor:10000)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47405 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Normalization -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -o /data/asap2/users/462/o8vex4/normalization/47405/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/462/o8vex4/normalization/47405/exec.out 2> /data/asap2/users/462/o8vex4/normalization/47405/exec.err'"


## ----------------------------------------------------------------
## Run 47406  Scaling  (Scaling #1 asap_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/scaling/47406/"

## Running Scaling [47406] [Scaling #1 asap_seurat] (input_matrix:normalization #1 do_scale:true do_center:true scale_max:10)
echo '-> Running Scaling [47406] [Scaling #1 asap_seurat] (input_matrix:normalization #1 do_scale:true do_center:true scale_max:10)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47406 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Scaling -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -o /data/asap2/users/462/o8vex4/scaling/47406/output.json -iAnnot /layers/norm_1_asap_seurat -oAnnot /layers/scaling_1_asap_seurat -scale true -center true -scaleMax 10  1> /data/asap2/users/462/o8vex4/scaling/47406/exec.out 2> /data/asap2/users/462/o8vex4/scaling/47406/exec.err'"


## ----------------------------------------------------------------
## Run 47407  Dimension reduction  (Dimension reduction #6 umap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/47407/"

## Running Dimension reduction [47407] [Dimension reduction #6 umap] (input_matrix:scaling #1 nber_dims:2 min_dist:0.1 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [47407] [Dimension reduction #6 umap] (input_matrix:scaling #1 nber_dims:2 min_dist:0.1 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47407 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/dim_reduction/32978 umap /layers/scaling_1_asap_seurat /col_attrs/_dr_6_umap_2D 2 0.1 30 correlation 1> /data/asap2/users/462/o8vex4/dim_reduction/47407/exec.out 2> /data/asap2/users/462/o8vex4/dim_reduction/47407/exec.err'"


## ----------------------------------------------------------------
## Run 47408  Cell selection  (Cell selection #1 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/cell_selection/47408/"

## Running Cell selection [47408] [Cell selection #1 cell_sel] ()
echo '-> Running Cell selection [47408] [Cell selection #1 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -meta /col_attrs/_dr_6_umap_2D.sel_1 -f /data/asap2/users/462/o8vex4/metadata/47408/list_cols.json '


## ----------------------------------------------------------------
## Run 47409  Cell selection  (Cell selection #2 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/cell_selection/47409/"

## Running Cell selection [47409] [Cell selection #2 cell_sel] ()
echo '-> Running Cell selection [47409] [Cell selection #2 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -meta /col_attrs/_dr_6_umap_2D.sel_2 -f /data/asap2/users/462/o8vex4/metadata/47409/list_cols.json '


## ----------------------------------------------------------------
## Run 47410  Cell selection  (Cell selection #3 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/cell_selection/47410/"

## Running Cell selection [47410] [Cell selection #3 cell_sel] ()
echo '-> Running Cell selection [47410] [Cell selection #3 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -meta /col_attrs/_dr_6_umap_2D.sel_3 -f /data/asap2/users/462/o8vex4/metadata/47410/list_cols.json '


## ----------------------------------------------------------------
## Run 47411  Cell selection  (Cell selection #4 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/cell_selection/47411/"

## Running Cell selection [47411] [Cell selection #4 cell_sel] ()
echo '-> Running Cell selection [47411] [Cell selection #4 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -meta /col_attrs/_dr_6_umap_2D.sel_4 -f /data/asap2/users/462/o8vex4/metadata/47411/list_cols.json '


## ----------------------------------------------------------------
## Run 47412  Differential expression  (Differential expression #1 wilcox_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/47412/"

## Running Differential expression [47412] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:cell_selection #1 group_ref:1 group_comp:0 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [47412] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:cell_selection #1 group_ref:1 group_comp:0 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47412 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/de/33037 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_1_wilcox_seurat null /col_attrs/_dr_6_umap_2D.sel_1 1 0 false 0.1 null 1.3 null 1> /data/asap2/users/462/o8vex4/de/47412/exec.out 2> /data/asap2/users/462/o8vex4/de/47412/exec.err'"


## ----------------------------------------------------------------
## Run 47413  Differential expression  (Differential expression #2 wilcox_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/47413/"

## Running Differential expression [47413] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:cell_selection #4 group_ref:1 group_comp:0 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [47413] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:cell_selection #4 group_ref:1 group_comp:0 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47413 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/de/33038 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_2_wilcox_seurat null /col_attrs/_dr_6_umap_2D.sel_4 1 0 false 0.1 null 1.3 null 1> /data/asap2/users/462/o8vex4/de/47413/exec.out 2> /data/asap2/users/462/o8vex4/de/47413/exec.err'"


## ----------------------------------------------------------------
## Run 47414  Differential expression  (Differential expression #3 wilcox_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/47414/"

## Running Differential expression [47414] [Differential expression #3 wilcox_seurat] (input_matrix:normalization #1 groups:cell_selection #2 group_ref:1 group_comp:0 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [47414] [Differential expression #3 wilcox_seurat] (input_matrix:normalization #1 groups:cell_selection #2 group_ref:1 group_comp:0 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47414 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/de/33039 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_3_wilcox_seurat null /col_attrs/_dr_6_umap_2D.sel_2 1 0 false 0.1 null 1.3 null 1> /data/asap2/users/462/o8vex4/de/47414/exec.out 2> /data/asap2/users/462/o8vex4/de/47414/exec.err'"


## ----------------------------------------------------------------
## Run 47415  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:v5 -c "mkdir -p $PROJECT_DIR/de/47415/"

## Running Differential expression [47415] [Differential expression #4 wilcox_seurat] (input_matrix:normalization #1 groups:cell_selection #3 group_ref:1 group_comp:0 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [47415] [Differential expression #4 wilcox_seurat] (input_matrix:normalization #1 groups:cell_selection #3 group_ref:1 group_comp:0 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47415 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/de/33040 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_4_wilcox_seurat null /col_attrs/_dr_6_umap_2D.sel_3 1 0 false 0.1 null 1.3 null 1> /data/asap2/users/462/o8vex4/de/47415/exec.out 2> /data/asap2/users/462/o8vex4/de/47415/exec.err'"


## ----------------------------------------------------------------
## Run 47416  Clustering  (Clustering #5 hclust)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/clustering/47416/"

## Running Clustering [47416] [Clustering #5 hclust] (input_matrix:dim_reduction #6 nb_clust:4 dist_method:euclidean clust_method:ward.D2)
echo '-> Running Clustering [47416] [Clustering #5 hclust] (input_matrix:dim_reduction #6 nb_clust:4 dist_method:euclidean clust_method:ward.D2)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47416 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla clustering.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/clustering/33046 hclust /col_attrs/_dr_6_umap_2D /col_attrs/_clust_5_hclust 4 euclidean ward.D2 1> /data/asap2/users/462/o8vex4/clustering/47416/exec.out 2> /data/asap2/users/462/o8vex4/clustering/47416/exec.err'"


## ----------------------------------------------------------------
## Run 47417  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:v5 -c "mkdir -p $PROJECT_DIR/de/47417/"

## Running Differential expression [47417] [Differential expression #5 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:1 group_comp:2 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [47417] [Differential expression #5 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:1 group_comp:2 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47417 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/de/33085 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_5_wilcox_seurat null /col_attrs/_clust_5_hclust 1 2 false 0.1 null 1.3 null 1> /data/asap2/users/462/o8vex4/de/47417/exec.out 2> /data/asap2/users/462/o8vex4/de/47417/exec.err'"


## ----------------------------------------------------------------
## Run 47418  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:v5 -c "mkdir -p $PROJECT_DIR/de/47418/"

## Running Differential expression [47418] [Differential expression #6 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:2 group_comp:1 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [47418] [Differential expression #6 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:2 group_comp:1 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47418 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/de/33086 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_6_wilcox_seurat null /col_attrs/_clust_5_hclust 2 1 false 0.1 null 1.3 null 1> /data/asap2/users/462/o8vex4/de/47418/exec.out 2> /data/asap2/users/462/o8vex4/de/47418/exec.err'"


## ----------------------------------------------------------------
## Run 47419  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:v5 -c "mkdir -p $PROJECT_DIR/de/47419/"

## Running Differential expression [47419] [Differential expression #7 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:4 group_comp:1 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [47419] [Differential expression #7 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:4 group_comp:1 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47419 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/de/33087 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_7_wilcox_seurat null /col_attrs/_clust_5_hclust 4 1 false 0.1 null 1.3 null 1> /data/asap2/users/462/o8vex4/de/47419/exec.out 2> /data/asap2/users/462/o8vex4/de/47419/exec.err'"


## ----------------------------------------------------------------
## Run 47420  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:v5 -c "mkdir -p $PROJECT_DIR/de/47420/"

## Running Differential expression [47420] [Differential expression #8 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:4 group_comp:2 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [47420] [Differential expression #8 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:4 group_comp:2 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47420 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/de/33088 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_8_wilcox_seurat null /col_attrs/_clust_5_hclust 4 2 false 0.1 null 1.3 null 1> /data/asap2/users/462/o8vex4/de/47420/exec.out 2> /data/asap2/users/462/o8vex4/de/47420/exec.err'"


## ----------------------------------------------------------------
## Run 47421  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:v5 -c "mkdir -p $PROJECT_DIR/de/47421/"

## Running Differential expression [47421] [Differential expression #9 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:3 group_comp:1 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [47421] [Differential expression #9 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:3 group_comp:1 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47421 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/de/33089 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_9_wilcox_seurat null /col_attrs/_clust_5_hclust 3 1 false 0.1 null 1.3 null 1> /data/asap2/users/462/o8vex4/de/47421/exec.out 2> /data/asap2/users/462/o8vex4/de/47421/exec.err'"


## ----------------------------------------------------------------
## Run 47422  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:v5 -c "mkdir -p $PROJECT_DIR/de/47422/"

## Running Differential expression [47422] [Differential expression #10 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:3 group_comp:2 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [47422] [Differential expression #10 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #5 group_ref:3 group_comp:2 min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47422 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/de/33090 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_10_wilcox_seurat null /col_attrs/_clust_5_hclust 3 2 false 0.1 null 1.3 null 1> /data/asap2/users/462/o8vex4/de/47422/exec.out 2> /data/asap2/users/462/o8vex4/de/47422/exec.err'"


## ----------------------------------------------------------------
## Run 47423  Gene Enrichment  (Gene Enrichment #1 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/47423/"

## Running Gene Enrichment [47423] [Gene Enrichment #1 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [47423] [Gene Enrichment #1 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47423 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -m fet -f /data/asap2/users/462/o8vex4/tmp/462_47412_2_0.05_filtered_ids.json -o /data/asap2/users/462/o8vex4/ge/47423/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/462/o8vex4/ge/47423/exec.out 2> /data/asap2/users/462/o8vex4/ge/47423/exec.err'"


## ----------------------------------------------------------------
## Run 47424  Gene Enrichment  (Gene Enrichment #2 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/47424/"

## Running Gene Enrichment [47424] [Gene Enrichment #2 basic] (input_de:de #2 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [47424] [Gene Enrichment #2 basic] (input_de:de #2 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47424 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -m fet -f /data/asap2/users/462/o8vex4/tmp/462_47413_2_0.05_filtered_ids.json -o /data/asap2/users/462/o8vex4/ge/47424/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/462/o8vex4/ge/47424/exec.out 2> /data/asap2/users/462/o8vex4/ge/47424/exec.err'"


## ----------------------------------------------------------------
## Run 47425  Gene Enrichment  (Gene Enrichment #3 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/47425/"

## Running Gene Enrichment [47425] [Gene Enrichment #3 basic] (input_de:de #3 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [47425] [Gene Enrichment #3 basic] (input_de:de #3 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47425 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -m fet -f /data/asap2/users/462/o8vex4/tmp/462_47414_2_0.05_filtered_ids.json -o /data/asap2/users/462/o8vex4/ge/47425/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/462/o8vex4/ge/47425/exec.out 2> /data/asap2/users/462/o8vex4/ge/47425/exec.err'"


## ----------------------------------------------------------------
## Run 47426  Gene Enrichment  (Gene Enrichment #4 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/47426/"

## Running Gene Enrichment [47426] [Gene Enrichment #4 basic] (input_de:de #4 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [47426] [Gene Enrichment #4 basic] (input_de:de #4 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47426 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -m fet -f /data/asap2/users/462/o8vex4/tmp/462_47415_2_0.05_filtered_ids.json -o /data/asap2/users/462/o8vex4/ge/47426/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/462/o8vex4/ge/47426/exec.out 2> /data/asap2/users/462/o8vex4/ge/47426/exec.err'"


## ----------------------------------------------------------------
## Run 47427  Gene Enrichment  (Gene Enrichment #5 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/47427/"

## Running Gene Enrichment [47427] [Gene Enrichment #5 basic] (input_de:de #5 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [47427] [Gene Enrichment #5 basic] (input_de:de #5 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47427 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -m fet -f /data/asap2/users/462/o8vex4/tmp/462_47417_2_0.05_filtered_ids.json -o /data/asap2/users/462/o8vex4/ge/47427/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/462/o8vex4/ge/47427/exec.out 2> /data/asap2/users/462/o8vex4/ge/47427/exec.err'"


## ----------------------------------------------------------------
## Run 47428  Gene Enrichment  (Gene Enrichment #6 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/47428/"

## Running Gene Enrichment [47428] [Gene Enrichment #6 basic] (input_de:de #6 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [47428] [Gene Enrichment #6 basic] (input_de:de #6 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47428 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -m fet -f /data/asap2/users/462/o8vex4/tmp/462_47418_2_0.05_filtered_ids.json -o /data/asap2/users/462/o8vex4/ge/47428/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/462/o8vex4/ge/47428/exec.out 2> /data/asap2/users/462/o8vex4/ge/47428/exec.err'"


## ----------------------------------------------------------------
## Run 47429  Gene Enrichment  (Gene Enrichment #7 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/47429/"

## Running Gene Enrichment [47429] [Gene Enrichment #7 basic] (input_de:de #7 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [47429] [Gene Enrichment #7 basic] (input_de:de #7 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47429 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -m fet -f /data/asap2/users/462/o8vex4/tmp/462_47419_2_0.05_filtered_ids.json -o /data/asap2/users/462/o8vex4/ge/47429/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/462/o8vex4/ge/47429/exec.out 2> /data/asap2/users/462/o8vex4/ge/47429/exec.err'"


## ----------------------------------------------------------------
## Run 47430  Gene Enrichment  (Gene Enrichment #8 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/47430/"

## Running Gene Enrichment [47430] [Gene Enrichment #8 basic] (input_de:de #8 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [47430] [Gene Enrichment #8 basic] (input_de:de #8 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47430 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -m fet -f /data/asap2/users/462/o8vex4/tmp/462_47420_2_0.05_filtered_ids.json -o /data/asap2/users/462/o8vex4/ge/47430/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/462/o8vex4/ge/47430/exec.out 2> /data/asap2/users/462/o8vex4/ge/47430/exec.err'"


## ----------------------------------------------------------------
## Run 47431  Gene Enrichment  (Gene Enrichment #9 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/47431/"

## Running Gene Enrichment [47431] [Gene Enrichment #9 basic] (input_de:de #9 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [47431] [Gene Enrichment #9 basic] (input_de:de #9 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47431 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -m fet -f /data/asap2/users/462/o8vex4/tmp/462_47421_2_0.05_filtered_ids.json -o /data/asap2/users/462/o8vex4/ge/47431/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/462/o8vex4/ge/47431/exec.out 2> /data/asap2/users/462/o8vex4/ge/47431/exec.err'"


## ----------------------------------------------------------------
## Run 47432  Gene Enrichment  (Gene Enrichment #10 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/47432/"

## Running Gene Enrichment [47432] [Gene Enrichment #10 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [47432] [Gene Enrichment #10 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47432 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -m fet -f /data/asap2/users/462/o8vex4/tmp/462_47422_2_0.05_filtered_ids.json -o /data/asap2/users/462/o8vex4/ge/47432/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/462/o8vex4/ge/47432/exec.out 2> /data/asap2/users/462/o8vex4/ge/47432/exec.err'"


## ----------------------------------------------------------------
## Run 47433  Dimension reduction  (Dimension reduction #18 umap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/47433/"

## Running Dimension reduction [47433] [Dimension reduction #18 umap] (input_matrix:scaling #1 nber_dims:2 min_dist:0.4 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [47433] [Dimension reduction #18 umap] (input_matrix:scaling #1 nber_dims:2 min_dist:0.4 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_47433 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/dim_reduction/33694 umap /layers/scaling_1_asap_seurat /col_attrs/_dr_18_umap_2D 2 0.4 30 correlation 1> /data/asap2/users/462/o8vex4/dim_reduction/47433/exec.out 2> /data/asap2/users/462/o8vex4/dim_reduction/47433/exec.err'"


## ----------------------------------------------------------------
## Run 50541  Dimension reduction  (Dimension reduction #19 umap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/50541/"

## Running Dimension reduction [50541] [Dimension reduction #19 umap] (input_matrix:gene_filtering #2 nber_dims:2 min_dist:0.1 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [50541] [Dimension reduction #19 umap] (input_matrix:gene_filtering #2 nber_dims:2 min_dist:0.1 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_50541 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/dim_reduction/50541 umap /matrix /col_attrs/_dr_19_umap_2D 2 0.1 30 correlation 1> /data/asap2/users/462/o8vex4/dim_reduction/50541/exec.out 2> /data/asap2/users/462/o8vex4/dim_reduction/50541/exec.err'"


## ----------------------------------------------------------------
## Run 50542  Dimension reduction  (Dimension reduction #20 umap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/50542/"

## Running Dimension reduction [50542] [Dimension reduction #20 umap] (input_matrix:gene_filtering #3 nber_dims:2 min_dist:0.1 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [50542] [Dimension reduction #20 umap] (input_matrix:gene_filtering #3 nber_dims:2 min_dist:0.1 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_50542 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/462/o8vex4/gene_filtering/47404/output.loom /data/asap2/users/462/o8vex4/dim_reduction/50542 umap /matrix /col_attrs/_dr_20_umap_2D 2 0.1 30 correlation 1> /data/asap2/users/462/o8vex4/dim_reduction/50542/exec.out 2> /data/asap2/users/462/o8vex4/dim_reduction/50542/exec.err'"


## ----------------------------------------------------------------
## Run 50543  Dimension reduction  (Dimension reduction #21 umap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/50543/"

## Running Dimension reduction [50543] [Dimension reduction #21 umap] (input_matrix:gene_filtering #2 nber_dims:3 min_dist:0.1 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [50543] [Dimension reduction #21 umap] (input_matrix:gene_filtering #2 nber_dims:3 min_dist:0.1 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_50543 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom /data/asap2/users/462/o8vex4/dim_reduction/50543 umap /matrix /col_attrs/_dr_21_umap_3D 3 0.1 30 correlation 1> /data/asap2/users/462/o8vex4/dim_reduction/50543/exec.out 2> /data/asap2/users/462/o8vex4/dim_reduction/50543/exec.err'"


## ----------------------------------------------------------------
## Run 50544  Dimension reduction  (Dimension reduction #22 umap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/50544/"

## Running Dimension reduction [50544] [Dimension reduction #22 umap] (input_matrix:gene_filtering #3 nber_dims:3 min_dist:0.1 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [50544] [Dimension reduction #22 umap] (input_matrix:gene_filtering #3 nber_dims:3 min_dist:0.1 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_50544 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/462/o8vex4/gene_filtering/47404/output.loom /data/asap2/users/462/o8vex4/dim_reduction/50544 umap /matrix /col_attrs/_dr_22_umap_3D 3 0.1 30 correlation 1> /data/asap2/users/462/o8vex4/dim_reduction/50544/exec.out 2> /data/asap2/users/462/o8vex4/dim_reduction/50544/exec.err'"


## ----------------------------------------------------------------
## Run 51345  Removing covariates  (Removing covariates #1 combat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/removing_covariates/51345/"

## Running Removing covariates [51345] [Removing covariates #1 combat] (input_matrix:normalization #1 covariates:gene_filtering #2)
echo '-> Running Removing covariates [51345] [Removing covariates #1 combat] (input_matrix:normalization #1 covariates:gene_filtering #2)'

## Command
sh -c ' '


## ----------------------------------------------------------------
## Run 66653  Module Score  (Module Score #1 seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/module_score/66653/"

## Running Module Score [66653] [Module Score #1 seurat] (input_matrix:normalization #1 geneset:gene_filtering #2 geneset_sel:TEC n_bins:24 n_background_genes:100 seed:42)
echo '-> Running Module Score [66653] [Module Score #1 seurat] (input_matrix:normalization #1 geneset:gene_filtering #2 geneset_sel:TEC n_bins:24 n_background_genes:100 seed:42)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_66653 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T ModuleScore -o /data/asap2/users/462/o8vex4/module_score/66653/output.json -oAnnot /col_attrs/_mscore_1_seurat -metadata /row_attrs/_Biotypes -sel TEC -m seurat -loom /data/asap2/users/462/o8vex4/gene_filtering/47403/output.loom -dataset /layers/norm_1_asap_seurat -seed 42 -nBins 24 -nBackgroundGenes 100  1> /data/asap2/users/462/o8vex4/module_score/66653/exec.out 2> /data/asap2/users/462/o8vex4/module_score/66653/exec.err'"