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

## CONFIGURATION (edit below to match your machine; lines until the separator)
export ASAP_PROJECTS_DIR=/asap_projects ## change this to write analysis results there (there will be subdirectory for each project key).
export LOOM_DIR=$ASAP_PROJECTS_DIR/loom_files
export ASAP_DATA_DB_HOST=localhost; export ASAP_DATA_DB_PORT=5432
export PSQL_DIR=/usr/pgsql-10/bin

## =========================================================

export PROJECT_DIR=$ASAP_PROJECTS_DIR/ymjqvi
## Pull Docker images (must run before any docker run in this script)

docker pull fabdavid/asap_run:v5

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

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

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

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

## Step output directories (one folder per pipeline step that has runs)
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/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/"

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

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


## ----------------------------------------------------------------
## Run 15297  Cell filtering  (Cell filtering #1 qc_plots)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/cell_filtering/15297/"

## writing file $PROJECT_DIR/cell_filtering/15297/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/15297/discarded_cols.json'
docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "echo '{"discarded_cols":["2","62","333","425","616","710","954","1015","1207","1512","2072","2287","2308","2406","2455","2475","2951","2952","3001","3055","3246","3290","3858","3953","4249","4309","4413","4585","4599","4607","4728","4769","4837","4849","4872","4965","4977","5081","5184","5290","5512","6242","6353","6372","6426","6921","7061","7129","7142","7146","7272","7447","7582","8039","8047","8429","8456","8501","8504","8683","8691","8941","8972","9057","9111","9638","9791","9815","9977","10409","10564","10590","10648","10860","10890","11030","11079","11148","11457","11490","11518","11637","11743","11906","12213","12226","12369","12707","12852","12870","12946","13168","13464","13544","13606","13665","13857","14022","14104","14183","14353","14359","14429","14643","14940","14958","14978","15006","15307","15444","15561","15570","15660","15718","15950","16130","16371","16416","16471","16557","16593","16699","16703","16800","16869","16968","17084","17192","17357","17383","17674","17769","17810","17898","17916","17956","18126","18357","18526","18555","18865","19014","19253","19277","19309","19579","19622","19770","19960","19989","20035","20080","20333","20516","20766","20897","21015","21043","21540","21774","21782","22317","22555","22632","22693","22863","22929","22973","22976","22987","23010","23101","23217","23219","23250","23365","23394","23441","23544","23597","23745","23989","24081","24131","24156","24248","24302","24403","24507","24629","24689","24873","25395","25468","25512","25540","25731","25755","25847","26207","26262","26277","26405","26789","27040","27116","27233","27278","27427","27637","27750","27841","27869","27895","28234","28392","28433","28522","28980","29017","29038","29281","29357","29371","29481","29585","29598","29640","29676","29878","29914","30022","30213","30214","30333","30360","30643","30685","30864","30915","31005","31022","31244","31325","31405","31531","31653","31769","31818","31864","32032","32312","32842","32991","33224","33381","33388","33391","33435","33451","33512","33659","33984","34022","34166","34201","34454","34466","34476","34497","34502","34766","34962","34985","35080","35127","35130","35140","35184","35185","35281","35357","35586","35675","35700","35976","36154","36352","36516","36634","36666","36930","36975","37065","37131","37283","37441","37462","37553","37875","38139","38157","38159","38189","38200","38394","38461","38546","38777","38803","38858","39114","39390","39410","39452","40002","40067","40106","40221","40344","40402","40488","40692","40747","40836","41046","41279","41286","41295","41316","41984","42154","42155","42232","42477","42505","42693","42769","42878","43083","43128","43158","43264","43315","43553","43800","43989","44087","44101","44487","44591","44868","44874","44906","44908","45056","45199","45306","45331","45492","45513","45525","45560","45729","45764","45849","45869","46079","46089","46136","46349","46594","46649","46686","46755","46808","46955","46967","47046","47362","47376","47393","47540","47629","47748","47876","48102","48180","48293","48301","48431","48511","48538","48714","49120","49267","49414","49568","49758","49759","49926","50199","50322","50394","50414","50533","50622","50869","50967","51183","51194","51206","51337","51443","51779","51895","51912","52032","52123","52251","52262","52280","52282","52677","52725","52771","52955","53132","53284","53531","53661","54072","54239","54436","54523","54537","54573","55018","55039","55214","55369","55519","55655","55715","55739","55791","55931","55939","56106","56286","56393","56433","56680","56780","56828","56961","56983","57070","57332","57361","58075","58185","58298","58517","58588","58590","58595","58667","58688","58762","58833","59065","59104","59184","59318","59370","59478","59821","59972","59983","59999","60097","60159","60323","60369","60544","60748","60777","60918","61264","61405","61783","61799","61970","62106","62209","62220","62338","62343","62406","62609","62804","62817","62833","62914","62929","62976","63132","63223","63252","63332","63422","63536","63744","63782","63946","64017","64177","64312","64369","64422","64432","64548","64570","64911","65051","65118","65486","65488","65575","65635","65643","65979","66266","66433","66632","66648","66670","66769","66819","66899","66997","67175","67251","67296","67449","67509","67718","67886","68204","68604","68669","68679","68765","68910","68930","69362","69407","69436","69495","69563","70156","70253","70263","70281","70288","70311","70469","70694","70817","70884","70946","70951","71016","71028","71370","71439","71764","71859","71886","71959","72024","72107","72273","72367","72459","72568","72652","72899","72936","73140","73445","73472","73676","73692","73768","73988","73989","74038","74182","74199","74341","74355","74364","74475","74492","74938","75060","75485","75719","75952","75989","76045","76504","76611","76988","77149","77263","77264","77278","77452","77800","77841","77990","78185","78188","78243","78356","78484","78809","78813","79033","79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> $PROJECT_DIR/cell_filtering/15297/discarded_cols.json"

## writing file $PROJECT_DIR/cell_filtering/15297/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/15297/manually_discarded_cols.json'
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/15297/manually_discarded_cols.json"

## Running Cell filtering [15297] [Cell filtering #1 qc_plots] (depth:100 detected_genes:10 protein_coding_content:80 mito_content:100 ribo_content:20 nber_manually_discarded_cols:0 input_matrix:parsing)
echo '-> Running Cell filtering [15297] [Cell filtering #1 qc_plots] (depth:100 detected_genes:10 protein_coding_content:80 mito_content:100 ribo_content:20 nber_manually_discarded_cols:0 input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_15297 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FilterCols -loom /data/asap2/users/1/ymjqvi/parsing/output.loom -o /data/asap2/users/1/ymjqvi/cell_filtering/15297 -col_indexes_file /data/asap2/users/1/ymjqvi/cell_filtering/15297/discarded_cols.json  1> /data/asap2/users/1/ymjqvi/cell_filtering/15297/exec.out 2> /data/asap2/users/1/ymjqvi/cell_filtering/15297/exec.err'"


## ----------------------------------------------------------------
## Run 15303  Gene filtering  (Gene filtering #1 hvg_scanpy)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/gene_filtering/15303/"

## Running Gene filtering [15303] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1 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 [15303] [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_15303 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'python3 hvg_scanpy_opti.py  /data/asap2/users/1/ymjqvi/cell_filtering/15297/output.loom /matrix /data/asap2/users/1/ymjqvi/gene_filtering/15303 0.5 0.0125 3 Inf 20 None false 1> /data/asap2/users/1/ymjqvi/gene_filtering/15303/exec.out 2> /data/asap2/users/1/ymjqvi/gene_filtering/15303/exec.err'"


## ----------------------------------------------------------------
## Run 15311  Normalization  (Normalization #1 asap_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/normalization/15311/"

## Running Normalization [15311] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000)
echo '-> Running Normalization [15311] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_15311 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Normalization -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -o /data/asap2/users/1/ymjqvi/normalization/15311/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/ymjqvi/normalization/15311/exec.out 2> /data/asap2/users/1/ymjqvi/normalization/15311/exec.err'"


## ----------------------------------------------------------------
## Run 15312  Normalization  (Normalization #2 asap_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/normalization/15312/"

## Running Normalization [15312] [Normalization #2 asap_seurat] (input_matrix:cell_filtering #1 scale_factor:10000)
echo '-> Running Normalization [15312] [Normalization #2 asap_seurat] (input_matrix:cell_filtering #1 scale_factor:10000)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_15312 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Normalization -loom /data/asap2/users/1/ymjqvi/cell_filtering/15297/output.loom -o /data/asap2/users/1/ymjqvi/normalization/15312/output.json -oAnnot /layers/norm_2_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/ymjqvi/normalization/15312/exec.out 2> /data/asap2/users/1/ymjqvi/normalization/15312/exec.err'"


## ----------------------------------------------------------------
## Run 15314  Scaling  (Scaling #1 asap_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/scaling/15314/"

## Running Scaling [15314] [Scaling #1 asap_seurat] (input_matrix:normalization #1 do_scale:true do_center:true scale_max:10)
echo '-> Running Scaling [15314] [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_15314 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Scaling -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -o /data/asap2/users/1/ymjqvi/scaling/15314/output.json -iAnnot /layers/norm_1_asap_seurat -oAnnot /layers/scaling_1_asap_seurat -scale true -center true -scaleMax 10  1> /data/asap2/users/1/ymjqvi/scaling/15314/exec.out 2> /data/asap2/users/1/ymjqvi/scaling/15314/exec.err'"


## ----------------------------------------------------------------
## Run 15315  Dimension reduction  (Dimension reduction #1 inc_pca)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/15315/"

## Running Dimension reduction [15315] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1 nber_dims:50)
echo '-> Running Dimension reduction [15315] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1 nber_dims:50)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_15315 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'python3 pca_scanpy_opti.py  /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom /layers/scaling_1_asap_seurat /col_attrs/_dr_1_inc_pca_50D /data/asap2/users/1/ymjqvi/dim_reduction/15315/output.json 50 10000 20 1> /data/asap2/users/1/ymjqvi/dim_reduction/15315/exec.out 2> /data/asap2/users/1/ymjqvi/dim_reduction/15315/exec.err'"


## ----------------------------------------------------------------
## Run 15320  Dimension reduction  (Dimension reduction #4 tsne_scanpy)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/15320/"

## Running Dimension reduction [15320] [Dimension reduction #4 tsne_scanpy] (input_matrix:dim_reduction #1 nber_dims:2 perplexity:500 early_exag:12 learning_rate:200 random_state:0)
echo '-> Running Dimension reduction [15320] [Dimension reduction #4 tsne_scanpy] (input_matrix:dim_reduction #1 nber_dims:2 perplexity:500 early_exag:12 learning_rate:200 random_state:0)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_15320 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'python3 tsne_scanpy_opti.py  /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_4_tsne_scanpy_2D /data/asap2/users/1/ymjqvi/dim_reduction/15320/output.json 2 500 12 200 0 20 1> /data/asap2/users/1/ymjqvi/dim_reduction/15320/exec.out 2> /data/asap2/users/1/ymjqvi/dim_reduction/15320/exec.err'"


## ----------------------------------------------------------------
## Run 15321  Dimension reduction  (Dimension reduction #5 tsne_scanpy)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/15321/"

## Running Dimension reduction [15321] [Dimension reduction #5 tsne_scanpy] (input_matrix:dim_reduction #1 nber_dims:3 perplexity:500 early_exag:12 learning_rate:200 random_state:0)
echo '-> Running Dimension reduction [15321] [Dimension reduction #5 tsne_scanpy] (input_matrix:dim_reduction #1 nber_dims:3 perplexity:500 early_exag:12 learning_rate:200 random_state:0)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_15321 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'python3 tsne_scanpy_opti.py  /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_5_tsne_scanpy_3D /data/asap2/users/1/ymjqvi/dim_reduction/15321/output.json 3 500 12 200 0 20 1> /data/asap2/users/1/ymjqvi/dim_reduction/15321/exec.out 2> /data/asap2/users/1/ymjqvi/dim_reduction/15321/exec.err'"


## ----------------------------------------------------------------
## Run 16144  Clustering  (Clustering #1 seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/clustering/16144/"

## Running Clustering [16144] [Clustering #1 seurat] (input_matrix:dim_reduction #1 k:100 resolution:0.5 algorithm:louvain graph_type:nn)
echo '-> Running Clustering [16144] [Clustering #1 seurat] (input_matrix:dim_reduction #1 k:100 resolution:0.5 algorithm:louvain graph_type:nn)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16144 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla clustering.R  /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/clustering/16144 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_1_seurat 100 0.5 louvain nn 1> /data/asap2/users/1/ymjqvi/clustering/16144/exec.out 2> /data/asap2/users/1/ymjqvi/clustering/16144/exec.err'"


## ----------------------------------------------------------------
## Run 16154  Dimension reduction  (Dimension reduction #6 umap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/16154/"

## Running Dimension reduction [16154] [Dimension reduction #6 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.05 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [16154] [Dimension reduction #6 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.05 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16154 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/dim_reduction/16154 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_6_umap_2D 2 0.05 30 correlation 1> /data/asap2/users/1/ymjqvi/dim_reduction/16154/exec.out 2> /data/asap2/users/1/ymjqvi/dim_reduction/16154/exec.err'"


## ----------------------------------------------------------------
## Run 16155  Dimension reduction  (Dimension reduction #7 umap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/16155/"

## Running Dimension reduction [16155] [Dimension reduction #7 umap] (input_matrix:dim_reduction #1 nber_dims:3 min_dist:0.05 n_neighbors:30 metric:correlation)
echo '-> Running Dimension reduction [16155] [Dimension reduction #7 umap] (input_matrix:dim_reduction #1 nber_dims:3 min_dist:0.05 n_neighbors:30 metric:correlation)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16155 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla dimension_reduction.R  /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/dim_reduction/16155 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_7_umap_3D 3 0.05 30 correlation 1> /data/asap2/users/1/ymjqvi/dim_reduction/16155/exec.out 2> /data/asap2/users/1/ymjqvi/dim_reduction/16155/exec.err'"


## ----------------------------------------------------------------
## Run 24222  Differential expression  (Differential expression #1 wilcox_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/24222/"

## Running Differential expression [24222] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [24222] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 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_24222 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/de/24222 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_1_wilcox_seurat null /col_attrs/_clust_1_seurat 9 null false 0.1 null 1.3 null 1> /data/asap2/users/1/ymjqvi/de/24222/exec.out 2> /data/asap2/users/1/ymjqvi/de/24222/exec.err'"


## ----------------------------------------------------------------
## Run 24224  Differential expression  (Differential expression #2 wilcox_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/24224/"

## Running Differential expression [24224] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:12 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [24224] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 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_24224 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/de/24224 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_2_wilcox_seurat null /col_attrs/_clust_1_seurat 12 null false 0.1 null 1.3 null 1> /data/asap2/users/1/ymjqvi/de/24224/exec.out 2> /data/asap2/users/1/ymjqvi/de/24224/exec.err'"


## ----------------------------------------------------------------
## Run 24225  Differential expression  (Differential expression #3 wilcox_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/24225/"

## Running Differential expression [24225] [Differential expression #3 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:6 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [24225] [Differential expression #3 wilcox_seurat] (input_matrix:normalization #1 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_24225 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R  /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom /data/asap2/users/1/ymjqvi/de/24225 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_3_wilcox_seurat null /col_attrs/_clust_1_seurat 6 null false 0.1 null 1.3 null 1> /data/asap2/users/1/ymjqvi/de/24225/exec.out 2> /data/asap2/users/1/ymjqvi/de/24225/exec.err'"


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

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

## Running Differential expression [24228] [Differential expression #4 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 group_ref:12 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [24228] [Differential expression #4 wilcox_asap] (input_matrix:normalization #1 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_24228 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T DifferentialExpression -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -o /data/asap2/users/1/ymjqvi/de/24228 -m wilcox_asap -iAnnot /layers/norm_1_asap_seurat -oAnnot /row_attrs/_de_4_wilcox_asap -gAnnot /col_attrs/_clust_1_seurat -g1 12 -g2 null  1> /data/asap2/users/1/ymjqvi/de/24228/exec.out 2> /data/asap2/users/1/ymjqvi/de/24228/exec.err'"


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

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

## Running Differential expression [24229] [Differential expression #5 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 group_ref:6 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [24229] [Differential expression #5 wilcox_asap] (input_matrix:normalization #1 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_24229 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T DifferentialExpression -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -o /data/asap2/users/1/ymjqvi/de/24229 -m wilcox_asap -iAnnot /layers/norm_1_asap_seurat -oAnnot /row_attrs/_de_5_wilcox_asap -gAnnot /col_attrs/_clust_1_seurat -g1 6 -g2 null  1> /data/asap2/users/1/ymjqvi/de/24229/exec.out 2> /data/asap2/users/1/ymjqvi/de/24229/exec.err'"


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

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

## Running Differential expression [24230] [Differential expression #6 wilcox_asap] (input_matrix:normalization #1 groups:clustering #1 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)
echo '-> Running Differential expression [24230] [Differential expression #6 wilcox_asap] (input_matrix:normalization #1 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_24230 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T DifferentialExpression -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -o /data/asap2/users/1/ymjqvi/de/24230 -m wilcox_asap -iAnnot /layers/norm_1_asap_seurat -oAnnot /row_attrs/_de_6_wilcox_asap -gAnnot /col_attrs/_clust_1_seurat -g1 9 -g2 null  1> /data/asap2/users/1/ymjqvi/de/24230/exec.out 2> /data/asap2/users/1/ymjqvi/de/24230/exec.err'"


## ----------------------------------------------------------------
## Run 24234  Gene Enrichment  (Gene Enrichment #1 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24234/"

## Running Gene Enrichment [24234] [Gene Enrichment #1 basic] (input_de:de #6 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24234] [Gene Enrichment #1 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_24234 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24230_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24234/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24234/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24234/exec.err'"


## ----------------------------------------------------------------
## Run 24235  Gene Enrichment  (Gene Enrichment #2 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24235/"

## Running Gene Enrichment [24235] [Gene Enrichment #2 basic] (input_de:de #5 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24235] [Gene Enrichment #2 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_24235 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24229_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24235/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24235/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24235/exec.err'"


## ----------------------------------------------------------------
## Run 24236  Gene Enrichment  (Gene Enrichment #3 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24236/"

## Running Gene Enrichment [24236] [Gene Enrichment #3 basic] (input_de:de #4 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24236] [Gene Enrichment #3 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_24236 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24228_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24236/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24236/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24236/exec.err'"


## ----------------------------------------------------------------
## Run 24237  Gene Enrichment  (Gene Enrichment #4 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24237/"

## Running Gene Enrichment [24237] [Gene Enrichment #4 basic] (input_de:de #3 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24237] [Gene Enrichment #4 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_24237 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24225_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24237/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24237/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24237/exec.err'"


## ----------------------------------------------------------------
## Run 24238  Gene Enrichment  (Gene Enrichment #5 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24238/"

## Running Gene Enrichment [24238] [Gene Enrichment #5 basic] (input_de:de #2 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24238] [Gene Enrichment #5 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_24238 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24224_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24238/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24238/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24238/exec.err'"


## ----------------------------------------------------------------
## Run 24239  Gene Enrichment  (Gene Enrichment #6 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24239/"

## Running Gene Enrichment [24239] [Gene Enrichment #6 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24239] [Gene Enrichment #6 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_24239 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24222_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24239/output.json -max 500 -min 15 -adj fdr -geneset 2761 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24239/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24239/exec.err'"


## ----------------------------------------------------------------
## Run 24240  Gene Enrichment  (Gene Enrichment #7 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24240/"

## Running Gene Enrichment [24240] [Gene Enrichment #7 basic] (input_de:de #6 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24240] [Gene Enrichment #7 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_24240 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24230_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24240/output.json -max 500 -min 15 -adj fdr -geneset 52 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24240/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24240/exec.err'"


## ----------------------------------------------------------------
## Run 24241  Gene Enrichment  (Gene Enrichment #8 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24241/"

## Running Gene Enrichment [24241] [Gene Enrichment #8 basic] (input_de:de #5 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24241] [Gene Enrichment #8 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_24241 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24229_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24241/output.json -max 500 -min 15 -adj fdr -geneset 52 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24241/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24241/exec.err'"


## ----------------------------------------------------------------
## Run 24242  Gene Enrichment  (Gene Enrichment #9 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24242/"

## Running Gene Enrichment [24242] [Gene Enrichment #9 basic] (input_de:de #4 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24242] [Gene Enrichment #9 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_24242 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24228_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24242/output.json -max 500 -min 15 -adj fdr -geneset 52 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24242/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24242/exec.err'"


## ----------------------------------------------------------------
## Run 24243  Gene Enrichment  (Gene Enrichment #10 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24243/"

## Running Gene Enrichment [24243] [Gene Enrichment #10 basic] (input_de:de #3 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24243] [Gene Enrichment #10 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_24243 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24225_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24243/output.json -max 500 -min 15 -adj fdr -geneset 52 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24243/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24243/exec.err'"


## ----------------------------------------------------------------
## Run 24244  Gene Enrichment  (Gene Enrichment #11 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24244/"

## Running Gene Enrichment [24244] [Gene Enrichment #11 basic] (input_de:de #2 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24244] [Gene Enrichment #11 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_24244 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24224_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24244/output.json -max 500 -min 15 -adj fdr -geneset 52 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24244/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24244/exec.err'"


## ----------------------------------------------------------------
## Run 24245  Gene Enrichment  (Gene Enrichment #12 basic)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/24245/"

## Running Gene Enrichment [24245] [Gene Enrichment #12 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [24245] [Gene Enrichment #12 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_24245 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/ymjqvi/gene_filtering/15303/output.loom -m fet -f /data/asap2/users/1/ymjqvi/tmp/1_24222_filtered.json -o /data/asap2/users/1/ymjqvi/ge/24245/output.json -max 500 -min 15 -adj fdr -geneset 52 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/ymjqvi/ge/24245/exec.out 2> /data/asap2/users/1/ymjqvi/ge/24245/exec.err'"