## This script contains all commands executed in the PROJECT amc3um and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT amc3um / ASAP2**********************'
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/amc3um
## 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/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/scaling/ && 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/amc3um/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 11070  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/11070/"

## writing file $PROJECT_DIR/cell_filtering/11070/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/11070/discarded_cols.json'
docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "echo '{"discarded_cols":[1173,2281,132,1735,561,2344,1927,2188,708,8,659,1850,1336,2435,347,155,1856,1690,1736,1026,1172,205,1345,1363,53,1544,1656,2227,2377,2064,745,1304,1281,608,1314,1832,753,491,820,721,17,196,857,1717,22,43,74,90,92,116,121,202,207,250,261,268,284,334,341,413,555,558,577,606,638,675,679,720,722,866,893,925,956,1009,1069,1087,1091,1104,1122,1188,1199,1219,1261,1278,1279,1300,1306,1312,1333,1391,1413,1485,1558,1566,1628,1661,1664,1688,1702,1753,1777,1779,1786,1791,1834,1874,1906,1909,1931,1967,2043,2045,2054,2070,2144,2159,2163,2182,2210,2233,2292,2306,2325,2365,2411,2442,2478,2516,2537,231,476,1369,1756,55,106,201,291,306,310,320,357,365,368,373,393,414,452,481,517,538,594,618,690,744,787,911,958,962,983,1013,1050,1075,1110,1140,1177,1225,1236,1322,1335,1394,1433,1438,1453,1462,1471,1504,1556,1572,1577,1797,1853,1860,1861,1890,1912,1944,1963,2010,2022,2058,2059,2083,2140,2170,2177,2221,2242,2289,2301,2406,2456,2477,2484]}' > $PROJECT_DIR/cell_filtering/11070/discarded_cols.json"

## writing file $PROJECT_DIR/cell_filtering/11070/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/11070/manually_discarded_cols.json'
docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "echo '{"manually_discarded_cols":[]}' > $PROJECT_DIR/cell_filtering/11070/manually_discarded_cols.json"

## Running Cell filtering [11070] [Cell filtering #1 qc_plots] (depth:1000 detected_genes:1000 mito_content:40 protein_coding_content:40 ribo_content:0 nber_manually_discarded_cols:0 input_matrix:parsing)
echo '-> Running Cell filtering [11070] [Cell filtering #1 qc_plots] (depth:1000 detected_genes:1000 mito_content:40 protein_coding_content:40 ribo_content:0 nber_manually_discarded_cols:0 input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11070 --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/amc3um/parsing/output.loom -o /data/asap2/users/1/amc3um/cell_filtering/11070 -col_indexes_file /data/asap2/users/1/amc3um/cell_filtering/11070/discarded_cols.json  1> /data/asap2/users/1/amc3um/cell_filtering/11070/exec.out 2> /data/asap2/users/1/amc3um/cell_filtering/11070/exec.err'"


## ----------------------------------------------------------------
## Run 11071  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/11071/"

## Running Gene filtering [11071] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1 n_bins:20 n_top_genes:None is_logged:false min_disp:0.5 max_disp:Inf min_mean:0.0125 max_mean:3)
echo '-> Running Gene filtering [11071] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1 n_bins:20 n_top_genes:None 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_11071 --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/amc3um/cell_filtering/11070/output.loom /matrix /data/asap2/users/1/amc3um/gene_filtering/11071 0.5 0.0125 3 Inf 20 None false 1> /data/asap2/users/1/amc3um/gene_filtering/11071/exec.out 2> /data/asap2/users/1/amc3um/gene_filtering/11071/exec.err'"


## ----------------------------------------------------------------
## Run 11072  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/11072/"

## Running Gene filtering [11072] [Gene filtering #2 hvg] (input_matrix:cell_filtering #1 fdr:0.1 min_disp:0.5)
echo '-> Running Gene filtering [11072] [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_11072 --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/amc3um/cell_filtering/11070/output.loom /data/asap2/users/1/amc3um/gene_filtering/11072 hvg false 0.1 0.5 1> /data/asap2/users/1/amc3um/gene_filtering/11072/exec.out 2> /data/asap2/users/1/amc3um/gene_filtering/11072/exec.err'"


## ----------------------------------------------------------------
## Run 13031  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/13031/"

## Running Normalization [13031] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #2 scale_factor:10000)
echo '-> Running Normalization [13031] [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_13031 --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/amc3um/gene_filtering/11072/output.loom -o /data/asap2/users/1/amc3um/normalization/13031/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/amc3um/normalization/13031/exec.out 2> /data/asap2/users/1/amc3um/normalization/13031/exec.err'"


## ----------------------------------------------------------------
## Run 13032  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/13032/"

## Running Normalization [13032] [Normalization #2 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000)
echo '-> Running Normalization [13032] [Normalization #2 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13032 --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/amc3um/gene_filtering/11071/output.loom -o /data/asap2/users/1/amc3um/normalization/13032/output.json -oAnnot /layers/norm_2_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/amc3um/normalization/13032/exec.out 2> /data/asap2/users/1/amc3um/normalization/13032/exec.err'"


## ----------------------------------------------------------------
## Run 13033  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/13033/"

## Running Scaling [13033] [Scaling #1 asap_seurat] (input_matrix:normalization #2 do_scale:true do_center:true scale_max:10)
echo '-> Running Scaling [13033] [Scaling #1 asap_seurat] (input_matrix:normalization #2 do_scale:true do_center:true scale_max:10)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13033 --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/amc3um/gene_filtering/11071/output.loom -o /data/asap2/users/1/amc3um/scaling/13033/output.json -iAnnot /layers/norm_2_asap_seurat -oAnnot /layers/scaling_1_asap_seurat -scale true -center true -scaleMax 10  1> /data/asap2/users/1/amc3um/scaling/13033/exec.out 2> /data/asap2/users/1/amc3um/scaling/13033/exec.err'"


## ----------------------------------------------------------------
## Run 13034  Scaling  (Scaling #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/scaling/13034/"

## Running Scaling [13034] [Scaling #2 asap_seurat] (input_matrix:normalization #1 do_scale:true do_center:true scale_max:10)
echo '-> Running Scaling [13034] [Scaling #2 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_13034 --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/amc3um/gene_filtering/11072/output.loom -o /data/asap2/users/1/amc3um/scaling/13034/output.json -iAnnot /layers/norm_1_asap_seurat -oAnnot /layers/scaling_2_asap_seurat -scale true -center true -scaleMax 10  1> /data/asap2/users/1/amc3um/scaling/13034/exec.out 2> /data/asap2/users/1/amc3um/scaling/13034/exec.err'"


## ----------------------------------------------------------------
## Run 13035  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/13035/"

## Running Dimension reduction [13035] [Dimension reduction #1 inc_pca] (input_matrix:scaling #2 nber_dims:50)
echo '-> Running Dimension reduction [13035] [Dimension reduction #1 inc_pca] (input_matrix:scaling #2 nber_dims:50)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13035 --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/amc3um/gene_filtering/11072/output.loom /layers/scaling_2_asap_seurat /col_attrs/_dr_1_inc_pca_50D /data/asap2/users/1/amc3um/dim_reduction/13035/output.json 50 10000 20 1> /data/asap2/users/1/amc3um/dim_reduction/13035/exec.out 2> /data/asap2/users/1/amc3um/dim_reduction/13035/exec.err'"


## ----------------------------------------------------------------
## Run 13036  Dimension reduction  (Dimension reduction #2 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/13036/"

## Running Dimension reduction [13036] [Dimension reduction #2 inc_pca] (input_matrix:scaling #1 nber_dims:50)
echo '-> Running Dimension reduction [13036] [Dimension reduction #2 inc_pca] (input_matrix:scaling #1 nber_dims:50)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13036 --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/amc3um/gene_filtering/11071/output.loom /layers/scaling_1_asap_seurat /col_attrs/_dr_2_inc_pca_50D /data/asap2/users/1/amc3um/dim_reduction/13036/output.json 50 10000 20 1> /data/asap2/users/1/amc3um/dim_reduction/13036/exec.out 2> /data/asap2/users/1/amc3um/dim_reduction/13036/exec.err'"


## ----------------------------------------------------------------
## Run 13037  Dimension reduction  (Dimension reduction #3 umap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/13037/"

## Running Dimension reduction [13037] [Dimension reduction #3 umap] (input_matrix:dim_reduction #2 nber_dims:2 min_dist:0.2 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [13037] [Dimension reduction #3 umap] (input_matrix:dim_reduction #2 nber_dims:2 min_dist:0.2 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13037 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/dim_reduction/13037 umap /col_attrs/_dr_2_inc_pca_50D /col_attrs/_dr_3_umap_2D 2 0.2 30 correlation 1> /data/asap2/users/1/amc3um/dim_reduction/13037/exec.out 2> /data/asap2/users/1/amc3um/dim_reduction/13037/exec.err'"


## ----------------------------------------------------------------
## Run 13038  Dimension reduction  (Dimension reduction #4 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/13038/"

## Running Dimension reduction [13038] [Dimension reduction #4 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.2 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [13038] [Dimension reduction #4 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.2 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13038 --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/amc3um/gene_filtering/11072/output.loom /data/asap2/users/1/amc3um/dim_reduction/13038 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_4_umap_2D 2 0.2 30 correlation 1> /data/asap2/users/1/amc3um/dim_reduction/13038/exec.out 2> /data/asap2/users/1/amc3um/dim_reduction/13038/exec.err'"


## ----------------------------------------------------------------
## Run 13039  Dimension reduction  (Dimension reduction #5 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/13039/"

## Running Dimension reduction [13039] [Dimension reduction #5 umap] (input_matrix:dim_reduction #2 nber_dims:3 min_dist:0.2 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [13039] [Dimension reduction #5 umap] (input_matrix:dim_reduction #2 nber_dims:3 min_dist:0.2 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13039 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/dim_reduction/13039 umap /col_attrs/_dr_2_inc_pca_50D /col_attrs/_dr_5_umap_3D 3 0.2 30 correlation 1> /data/asap2/users/1/amc3um/dim_reduction/13039/exec.out 2> /data/asap2/users/1/amc3um/dim_reduction/13039/exec.err'"


## ----------------------------------------------------------------
## Run 13040  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:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/13040/"

## Running Dimension reduction [13040] [Dimension reduction #6 umap] (input_matrix:dim_reduction #1 nber_dims:3 min_dist:0.2 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [13040] [Dimension reduction #6 umap] (input_matrix:dim_reduction #1 nber_dims:3 min_dist:0.2 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13040 --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/amc3um/gene_filtering/11072/output.loom /data/asap2/users/1/amc3um/dim_reduction/13040 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_6_umap_3D 3 0.2 30 correlation 1> /data/asap2/users/1/amc3um/dim_reduction/13040/exec.out 2> /data/asap2/users/1/amc3um/dim_reduction/13040/exec.err'"


## ----------------------------------------------------------------
## Run 13041  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/13041/"

## Running Clustering [13041] [Clustering #1 seurat] (input_matrix:dim_reduction #2 k:20 resolution:0.8 algorithm:louvain)
echo '-> Running Clustering [13041] [Clustering #1 seurat] (input_matrix:dim_reduction #2 k:20 resolution:0.8 algorithm:louvain)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13041 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/clustering/13041 seurat /col_attrs/_dr_2_inc_pca_50D /col_attrs/_clust_1_seurat 20 0.8 louvain 1> /data/asap2/users/1/amc3um/clustering/13041/exec.out 2> /data/asap2/users/1/amc3um/clustering/13041/exec.err'"


## ----------------------------------------------------------------
## Run 13042  Clustering  (Clustering #2 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/13042/"

## Running Clustering [13042] [Clustering #2 seurat] (input_matrix:dim_reduction #1 k:20 resolution:0.8 algorithm:louvain)
echo '-> Running Clustering [13042] [Clustering #2 seurat] (input_matrix:dim_reduction #1 k:20 resolution:0.8 algorithm:louvain)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13042 --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/amc3um/gene_filtering/11072/output.loom /data/asap2/users/1/amc3um/clustering/13042 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_2_seurat 20 0.8 louvain 1> /data/asap2/users/1/amc3um/clustering/13042/exec.out 2> /data/asap2/users/1/amc3um/clustering/13042/exec.err'"


## ----------------------------------------------------------------
## Run 13043  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/13043/"

## Running Differential expression [13043] [Differential expression #1 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:1 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13043] [Differential expression #1 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:1 group_comp: 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_13043 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13043 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_1_wilcox-seurat null /col_attrs/_clust_1_seurat 1 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13043/exec.out 2> /data/asap2/users/1/amc3um/de/13043/exec.err'"


## ----------------------------------------------------------------
## Run 13044  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/13044/"

## Running Differential expression [13044] [Differential expression #2 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:2 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13044] [Differential expression #2 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:2 group_comp: 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_13044 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13044 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_2_wilcox-seurat null /col_attrs/_clust_1_seurat 2 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13044/exec.out 2> /data/asap2/users/1/amc3um/de/13044/exec.err'"


## ----------------------------------------------------------------
## Run 13045  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/13045/"

## Running Differential expression [13045] [Differential expression #3 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:3 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13045] [Differential expression #3 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:3 group_comp: 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_13045 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13045 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_3_wilcox-seurat null /col_attrs/_clust_1_seurat 3 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13045/exec.out 2> /data/asap2/users/1/amc3um/de/13045/exec.err'"


## ----------------------------------------------------------------
## Run 13046  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/13046/"

## Running Differential expression [13046] [Differential expression #4 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:4 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13046] [Differential expression #4 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:4 group_comp: 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_13046 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13046 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_4_wilcox-seurat null /col_attrs/_clust_1_seurat 4 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13046/exec.out 2> /data/asap2/users/1/amc3um/de/13046/exec.err'"


## ----------------------------------------------------------------
## Run 13047  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/13047/"

## Running Differential expression [13047] [Differential expression #5 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:5 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13047] [Differential expression #5 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:5 group_comp: 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_13047 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13047 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_5_wilcox-seurat null /col_attrs/_clust_1_seurat 5 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13047/exec.out 2> /data/asap2/users/1/amc3um/de/13047/exec.err'"


## ----------------------------------------------------------------
## Run 13048  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/13048/"

## Running Differential expression [13048] [Differential expression #6 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:6 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13048] [Differential expression #6 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:6 group_comp: 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_13048 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13048 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_6_wilcox-seurat null /col_attrs/_clust_1_seurat 6 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13048/exec.out 2> /data/asap2/users/1/amc3um/de/13048/exec.err'"


## ----------------------------------------------------------------
## Run 13049  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/13049/"

## Running Differential expression [13049] [Differential expression #7 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:7 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13049] [Differential expression #7 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:7 group_comp: 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_13049 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13049 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_7_wilcox-seurat null /col_attrs/_clust_1_seurat 7 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13049/exec.out 2> /data/asap2/users/1/amc3um/de/13049/exec.err'"


## ----------------------------------------------------------------
## Run 13050  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/13050/"

## Running Differential expression [13050] [Differential expression #8 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:8 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13050] [Differential expression #8 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:8 group_comp: 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_13050 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13050 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_8_wilcox-seurat null /col_attrs/_clust_1_seurat 8 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13050/exec.out 2> /data/asap2/users/1/amc3um/de/13050/exec.err'"


## ----------------------------------------------------------------
## Run 13051  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/13051/"

## Running Differential expression [13051] [Differential expression #9 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13051] [Differential expression #9 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:9 group_comp: 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_13051 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13051 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_9_wilcox-seurat null /col_attrs/_clust_1_seurat 9 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13051/exec.out 2> /data/asap2/users/1/amc3um/de/13051/exec.err'"


## ----------------------------------------------------------------
## Run 13052  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/13052/"

## Running Differential expression [13052] [Differential expression #10 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:10 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13052] [Differential expression #10 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:10 group_comp: 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_13052 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13052 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_10_wilcox-seurat null /col_attrs/_clust_1_seurat 10 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13052/exec.out 2> /data/asap2/users/1/amc3um/de/13052/exec.err'"


## ----------------------------------------------------------------
## Run 13053  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/13053/"

## Running Differential expression [13053] [Differential expression #11 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:11 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13053] [Differential expression #11 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:11 group_comp: 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_13053 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13053 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_11_wilcox-seurat null /col_attrs/_clust_1_seurat 11 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13053/exec.out 2> /data/asap2/users/1/amc3um/de/13053/exec.err'"


## ----------------------------------------------------------------
## Run 13054  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/13054/"

## Running Differential expression [13054] [Differential expression #12 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:12 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13054] [Differential expression #12 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:12 group_comp: 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_13054 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13054 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_12_wilcox-seurat null /col_attrs/_clust_1_seurat 12 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13054/exec.out 2> /data/asap2/users/1/amc3um/de/13054/exec.err'"


## ----------------------------------------------------------------
## Run 13055  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/13055/"

## Running Differential expression [13055] [Differential expression #13 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:13 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13055] [Differential expression #13 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:13 group_comp: 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_13055 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13055 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_13_wilcox-seurat null /col_attrs/_clust_1_seurat 13 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13055/exec.out 2> /data/asap2/users/1/amc3um/de/13055/exec.err'"


## ----------------------------------------------------------------
## Run 13056  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/13056/"

## Running Differential expression [13056] [Differential expression #14 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:14 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13056] [Differential expression #14 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:14 group_comp: 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_13056 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13056 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_14_wilcox-seurat null /col_attrs/_clust_1_seurat 14 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13056/exec.out 2> /data/asap2/users/1/amc3um/de/13056/exec.err'"


## ----------------------------------------------------------------
## Run 13057  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/13057/"

## Running Differential expression [13057] [Differential expression #15 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:15 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13057] [Differential expression #15 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:15 group_comp: 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_13057 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13057 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_15_wilcox-seurat null /col_attrs/_clust_1_seurat 15 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13057/exec.out 2> /data/asap2/users/1/amc3um/de/13057/exec.err'"


## ----------------------------------------------------------------
## Run 13058  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/13058/"

## Running Differential expression [13058] [Differential expression #16 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:16 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13058] [Differential expression #16 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:16 group_comp: 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_13058 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13058 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_16_wilcox-seurat null /col_attrs/_clust_1_seurat 16 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13058/exec.out 2> /data/asap2/users/1/amc3um/de/13058/exec.err'"


## ----------------------------------------------------------------
## Run 13059  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/13059/"

## Running Differential expression [13059] [Differential expression #17 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:17 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13059] [Differential expression #17 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:17 group_comp: 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_13059 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13059 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_17_wilcox-seurat null /col_attrs/_clust_1_seurat 17 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13059/exec.out 2> /data/asap2/users/1/amc3um/de/13059/exec.err'"


## ----------------------------------------------------------------
## Run 13060  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/13060/"

## Running Differential expression [13060] [Differential expression #18 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:18 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [13060] [Differential expression #18 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:18 group_comp: 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_13060 --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/amc3um/gene_filtering/11071/output.loom /data/asap2/users/1/amc3um/de/13060 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_18_wilcox-seurat null /col_attrs/_clust_1_seurat 18 null false 0.1 null 1.3 null 1> /data/asap2/users/1/amc3um/de/13060/exec.out 2> /data/asap2/users/1/amc3um/de/13060/exec.err'"


## ----------------------------------------------------------------
## Run 13061  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:v4 -c "mkdir -p $PROJECT_DIR/ge/13061/"

## Running Gene Enrichment [13061] [Gene Enrichment #1 basic] (input_de:de #18 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13061] [Gene Enrichment #1 basic] (input_de:de #18 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_13061 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13060_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13061/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13061/exec.out 2> /data/asap2/users/1/amc3um/ge/13061/exec.err'"


## ----------------------------------------------------------------
## Run 13062  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:v4 -c "mkdir -p $PROJECT_DIR/ge/13062/"

## Running Gene Enrichment [13062] [Gene Enrichment #2 basic] (input_de:de #17 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13062] [Gene Enrichment #2 basic] (input_de:de #17 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_13062 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13059_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13062/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13062/exec.out 2> /data/asap2/users/1/amc3um/ge/13062/exec.err'"


## ----------------------------------------------------------------
## Run 13063  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:v4 -c "mkdir -p $PROJECT_DIR/ge/13063/"

## Running Gene Enrichment [13063] [Gene Enrichment #3 basic] (input_de:de #16 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13063] [Gene Enrichment #3 basic] (input_de:de #16 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_13063 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13058_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13063/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13063/exec.out 2> /data/asap2/users/1/amc3um/ge/13063/exec.err'"


## ----------------------------------------------------------------
## Run 13064  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:v4 -c "mkdir -p $PROJECT_DIR/ge/13064/"

## Running Gene Enrichment [13064] [Gene Enrichment #4 basic] (input_de:de #15 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13064] [Gene Enrichment #4 basic] (input_de:de #15 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_13064 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13057_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13064/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13064/exec.out 2> /data/asap2/users/1/amc3um/ge/13064/exec.err'"


## ----------------------------------------------------------------
## Run 13065  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:v4 -c "mkdir -p $PROJECT_DIR/ge/13065/"

## Running Gene Enrichment [13065] [Gene Enrichment #5 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13065] [Gene Enrichment #5 basic] (input_de:de #14 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_13065 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13056_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13065/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13065/exec.out 2> /data/asap2/users/1/amc3um/ge/13065/exec.err'"


## ----------------------------------------------------------------
## Run 13066  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:v4 -c "mkdir -p $PROJECT_DIR/ge/13066/"

## Running Gene Enrichment [13066] [Gene Enrichment #6 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13066] [Gene Enrichment #6 basic] (input_de:de #13 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_13066 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13055_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13066/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13066/exec.out 2> /data/asap2/users/1/amc3um/ge/13066/exec.err'"


## ----------------------------------------------------------------
## Run 13067  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:v4 -c "mkdir -p $PROJECT_DIR/ge/13067/"

## Running Gene Enrichment [13067] [Gene Enrichment #7 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13067] [Gene Enrichment #7 basic] (input_de:de #12 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_13067 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13054_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13067/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13067/exec.out 2> /data/asap2/users/1/amc3um/ge/13067/exec.err'"


## ----------------------------------------------------------------
## Run 13068  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:v4 -c "mkdir -p $PROJECT_DIR/ge/13068/"

## Running Gene Enrichment [13068] [Gene Enrichment #8 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13068] [Gene Enrichment #8 basic] (input_de:de #11 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_13068 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13053_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13068/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13068/exec.out 2> /data/asap2/users/1/amc3um/ge/13068/exec.err'"


## ----------------------------------------------------------------
## Run 13069  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:v4 -c "mkdir -p $PROJECT_DIR/ge/13069/"

## Running Gene Enrichment [13069] [Gene Enrichment #9 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13069] [Gene Enrichment #9 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_13069 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13052_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13069/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13069/exec.out 2> /data/asap2/users/1/amc3um/ge/13069/exec.err'"


## ----------------------------------------------------------------
## Run 13070  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:v4 -c "mkdir -p $PROJECT_DIR/ge/13070/"

## Running Gene Enrichment [13070] [Gene Enrichment #10 basic] (input_de:de #9 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13070] [Gene Enrichment #10 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_13070 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13051_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13070/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13070/exec.out 2> /data/asap2/users/1/amc3um/ge/13070/exec.err'"


## ----------------------------------------------------------------
## Run 13071  Gene Enrichment  (Gene Enrichment #11 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/13071/"

## Running Gene Enrichment [13071] [Gene Enrichment #11 basic] (input_de:de #8 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13071] [Gene Enrichment #11 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_13071 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13050_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13071/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13071/exec.out 2> /data/asap2/users/1/amc3um/ge/13071/exec.err'"


## ----------------------------------------------------------------
## Run 13072  Gene Enrichment  (Gene Enrichment #12 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/13072/"

## Running Gene Enrichment [13072] [Gene Enrichment #12 basic] (input_de:de #7 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13072] [Gene Enrichment #12 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_13072 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13049_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13072/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13072/exec.out 2> /data/asap2/users/1/amc3um/ge/13072/exec.err'"


## ----------------------------------------------------------------
## Run 13073  Gene Enrichment  (Gene Enrichment #13 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/13073/"

## Running Gene Enrichment [13073] [Gene Enrichment #13 basic] (input_de:de #6 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13073] [Gene Enrichment #13 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_13073 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13048_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13073/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13073/exec.out 2> /data/asap2/users/1/amc3um/ge/13073/exec.err'"


## ----------------------------------------------------------------
## Run 13074  Gene Enrichment  (Gene Enrichment #14 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/13074/"

## Running Gene Enrichment [13074] [Gene Enrichment #14 basic] (input_de:de #5 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13074] [Gene Enrichment #14 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_13074 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13047_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13074/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13074/exec.out 2> /data/asap2/users/1/amc3um/ge/13074/exec.err'"


## ----------------------------------------------------------------
## Run 13075  Gene Enrichment  (Gene Enrichment #15 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/13075/"

## Running Gene Enrichment [13075] [Gene Enrichment #15 basic] (input_de:de #4 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13075] [Gene Enrichment #15 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_13075 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13046_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13075/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13075/exec.out 2> /data/asap2/users/1/amc3um/ge/13075/exec.err'"


## ----------------------------------------------------------------
## Run 13076  Gene Enrichment  (Gene Enrichment #16 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/13076/"

## Running Gene Enrichment [13076] [Gene Enrichment #16 basic] (input_de:de #3 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13076] [Gene Enrichment #16 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_13076 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13045_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13076/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13076/exec.out 2> /data/asap2/users/1/amc3um/ge/13076/exec.err'"


## ----------------------------------------------------------------
## Run 13077  Gene Enrichment  (Gene Enrichment #17 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/13077/"

## Running Gene Enrichment [13077] [Gene Enrichment #17 basic] (input_de:de #2 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13077] [Gene Enrichment #17 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_13077 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13044_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13077/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13077/exec.out 2> /data/asap2/users/1/amc3um/ge/13077/exec.err'"


## ----------------------------------------------------------------
## Run 13078  Gene Enrichment  (Gene Enrichment #18 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/13078/"

## Running Gene Enrichment [13078] [Gene Enrichment #18 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [13078] [Gene Enrichment #18 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_13078 --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 Enrichment -loom /data/asap2/users/1/amc3um/gene_filtering/11071/output.loom -m fet -f /data/asap2/users/1/amc3um/tmp/1_13043_2_0.05_filtered_ids.json -o /data/asap2/users/1/amc3um/ge/13078/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4  1> /data/asap2/users/1/amc3um/ge/13078/exec.out 2> /data/asap2/users/1/amc3um/ge/13078/exec.err'"


## ----------------------------------------------------------------
## Run 711336  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/711336/"

## Running Find markers [711336] [Find markers #1 asap_markers] (input_matrix:gene_filtering #1)
echo '-> Running Find markers [711336] [Find markers #1 asap_markers] (input_matrix:gene_filtering #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_711336 --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/amc3um/gene_filtering/11071/output.loom -o /data/asap2/users/1/amc3um/markers/711336 --iAnnot /col_attrs/_clust_1_seurat --id 47769 --is_count_table false  1> /data/asap2/users/1/amc3um/markers/711336/exec.out 2> /data/asap2/users/1/amc3um/markers/711336/exec.err'"