## This script contains all commands executed in the PROJECT rzy6gj and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT rzy6gj / ASAP95**********************'
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/rzy6gj
## Pull Docker images (must run before any docker run in this script)

docker pull fabdavid/asap_run:v6

## Host LOOM staging directory (inside Docker volume)
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -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_v6; then echo 'Create database asap_data_v6'; echo '$PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v6'; $PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v6; echo 'wget -qO - https://asap.epfl.ch/dumps/asap_data_v6.sql.gz | gunzip | grep -v \'AS integer\' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v6'; wget -qO - https://asap.epfl.ch/dumps/asap_data_v6.sql.gz | gunzip | grep -v 'AS integer' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v6; fi

## Project directory on the shared volume
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -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:v6 -c "mkdir -p $PROJECT_DIR/cell_filtering/ && mkdir -p $PROJECT_DIR/cell_selection/ && mkdir -p $PROJECT_DIR/scaling/ && mkdir -p $PROJECT_DIR/markers/ && mkdir -p $PROJECT_DIR/de/ && mkdir -p $PROJECT_DIR/pca/ && mkdir -p $PROJECT_DIR/umap/ && mkdir -p $PROJECT_DIR/clustering/ && mkdir -p $PROJECT_DIR/module_score/ && mkdir -p $PROJECT_DIR/tsne/ && mkdir -p $PROJECT_DIR/normalization/ && mkdir -p $PROJECT_DIR/ge/ && mkdir -p $PROJECT_DIR/hvg/ && mkdir -p $PROJECT_DIR/parsing/"

## 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:v6 -c "wget -qO $PROJECT_DIR/parsing/output.loom 'https://asap.epfl.ch/projects/rzy6gj/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 588195  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:v6 -c "mkdir -p $PROJECT_DIR/cell_filtering/588195/"

## writing file $PROJECT_DIR/cell_filtering/588195/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/588195/discarded_cols.json'
docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "echo '{"discarded_cols":["7","11","23","24","28","35","37","47","58","60","61","64","72","73","74","84","85","95","103","108","109","120","129","135","138","152","168","173","187","191","192","213","214","217","228","232","235","240","256","315","318","334","340","342","346","352","359","361","362","386","394","395","422","433","439","440","443","449","454","468","475","479","482","486","487","496","498","509","510","513","531","537","561","571","574","579","584","587","605","617","634","647","657","663","664","665","669","679","682","697","700","706","713","726","745","771","778","780","804","805","811","813","819","824","844","847","856","866","878","879","881","882","887","894","913","923","930","934","939","946","949","956","960","962","970","981","982","989"]}' > $PROJECT_DIR/cell_filtering/588195/discarded_cols.json"

## writing file $PROJECT_DIR/cell_filtering/588195/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/588195/manually_discarded_cols.json'
docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "echo '{"manually_discarded_cols":[]}' > $PROJECT_DIR/cell_filtering/588195/manually_discarded_cols.json"

## Running Cell filtering [588195] [Cell filtering #1 qc_plots] (depth:1000 detected_genes:500 protein_coding_content:80 mito_content:20 ribo_content:40 nber_manually_discarded_cols:0 input_matrix:parsing manual_selection:)
echo '-> Running Cell filtering [588195] [Cell filtering #1 qc_plots] (depth:1000 detected_genes:500 protein_coding_content:80 mito_content:20 ribo_content:40 nber_manually_discarded_cols:0 input_matrix:parsing manual_selection:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588195 --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:v6 -c "sh -c 'java -jar /srv/ASAP.jar -T FilterCols -loom /data/asap2/users/1474/rzy6gj/parsing/output.loom -o /data/asap2/users/1474/rzy6gj/cell_filtering/588195 -col_indexes_file /data/asap2/users/1474/rzy6gj/cell_filtering/588195/discarded_cols.json  1> /data/asap2/users/1474/rzy6gj/cell_filtering/588195/exec.out 2> /data/asap2/users/1474/rzy6gj/cell_filtering/588195/exec.err'"


## ----------------------------------------------------------------
## Run 588196  Normalization  (Normalization #1 seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/normalization/588196/"

## Running Normalization [588196] [Normalization #1 seurat] (input_matrix:cell_filtering #1)
echo '-> Running Normalization [588196] [Normalization #1 seurat] (input_matrix:cell_filtering #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588196 --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:v6 -c "sh -c 'Rscript --vanilla normalization.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom /matrix /layers/norm_1_seurat /data/asap2/users/1474/rzy6gj/normalization/588196 1> /data/asap2/users/1474/rzy6gj/normalization/588196/exec.out 2> /data/asap2/users/1474/rzy6gj/normalization/588196/exec.err'"


## ----------------------------------------------------------------
## Run 588197  HVG  (HVG #1 vst)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/hvg/588197/"

## Running HVG [588197] [HVG #1 vst] (input_matrix:normalization #1 nber_features:2000)
echo '-> Running HVG [588197] [HVG #1 vst] (input_matrix:normalization #1 nber_features:2000)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588197 --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:v6 -c "sh -c 'Rscript --vanilla hvg.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom /matrix /layers/norm_1_seurat /row_attrs/hvg_1_vst /data/asap2/users/1474/rzy6gj/hvg/588197 vst 2000 1> /data/asap2/users/1474/rzy6gj/hvg/588197/exec.out 2> /data/asap2/users/1474/rzy6gj/hvg/588197/exec.err'"


## ----------------------------------------------------------------
## Run 588198  Scaling  (Scaling #1 seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/scaling/588198/"

## Running Scaling [588198] [Scaling #1 seurat] (input_matrix:normalization #1)
echo '-> Running Scaling [588198] [Scaling #1 seurat] (input_matrix:normalization #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588198 --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:v6 -c "sh -c 'Rscript --vanilla scaling.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom /matrix /layers/norm_1_seurat /layers/scaling_1_seurat /data/asap2/users/1474/rzy6gj/scaling/588198  1> /data/asap2/users/1474/rzy6gj/scaling/588198/exec.out 2> /data/asap2/users/1474/rzy6gj/scaling/588198/exec.err'"


## ----------------------------------------------------------------
## Run 588199  PCA  (PCA #1 pca_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/pca/588199/"

## Running PCA [588199] [PCA #1 pca_seurat] (input_matrix:scaling #1 variable_features_dataset:hvg #1 nber_dims:50)
echo '-> Running PCA [588199] [PCA #1 pca_seurat] (input_matrix:scaling #1 variable_features_dataset:hvg #1 nber_dims:50)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588199 --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:v6 -c "sh -c 'Rscript --vanilla pca.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom /matrix /layers/norm_1_seurat /layers/scaling_1_seurat /row_attrs/hvg_1_vst /col_attrs/_pca_1_pca_seurat_50D /data/asap2/users/1474/rzy6gj/pca/588199 50 1> /data/asap2/users/1474/rzy6gj/pca/588199/exec.out 2> /data/asap2/users/1474/rzy6gj/pca/588199/exec.err'"


## ----------------------------------------------------------------
## Run 588200  Cell selection  (Cell selection #1 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588200/"

## Running Cell selection [588200] [Cell selection #1 cell_sel] ()
echo '-> Running Cell selection [588200] [Cell selection #1 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_pca_1_pca_seurat_50D.sel_1 -f /data/asap2/users/1474/rzy6gj/metadata/588200/list_cols.json '


## ----------------------------------------------------------------
## Run 588201  Cell selection  (Cell selection #2 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588201/"

## Running Cell selection [588201] [Cell selection #2 cell_sel] ()
echo '-> Running Cell selection [588201] [Cell selection #2 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_pca_1_pca_seurat_50D.sel_2 -f /data/asap2/users/1474/rzy6gj/metadata/588201/list_cols.json '


## ----------------------------------------------------------------
## Run 588202  Cell selection  (Cell selection #3 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588202/"

## Running Cell selection [588202] [Cell selection #3 cell_sel] ()
echo '-> Running Cell selection [588202] [Cell selection #3 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_pca_1_pca_seurat_50D.sel_3 -f /data/asap2/users/1474/rzy6gj/metadata/588202/list_cols.json '


## ----------------------------------------------------------------
## Run 588203  Cell selection  (Cell selection #4 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588203/"

## Running Cell selection [588203] [Cell selection #4 cell_sel] ()
echo '-> Running Cell selection [588203] [Cell selection #4 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_pca_1_pca_seurat_50D.sel_4 -f /data/asap2/users/1474/rzy6gj/metadata/588203/list_cols.json '


## ----------------------------------------------------------------
## Run 588204  Cell selection  (Cell selection #5 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588204/"

## Running Cell selection [588204] [Cell selection #5 cell_sel] ()
echo '-> Running Cell selection [588204] [Cell selection #5 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_pca_1_pca_seurat_50D.sel_5 -f /data/asap2/users/1474/rzy6gj/metadata/588204/list_cols.json '


## ----------------------------------------------------------------
## Run 588205  Cell selection  (Cell selection #6 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588205/"

## Running Cell selection [588205] [Cell selection #6 cell_sel] ()
echo '-> Running Cell selection [588205] [Cell selection #6 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_pca_1_pca_seurat_50D.sel_6 -f /data/asap2/users/1474/rzy6gj/metadata/588205/list_cols.json '


## ----------------------------------------------------------------
## Run 588206  Cell selection  (Cell selection #7 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588206/"

## Running Cell selection [588206] [Cell selection #7 cell_sel] ()
echo '-> Running Cell selection [588206] [Cell selection #7 cell_sel] ()'

## Command
sh -c ' '


## ----------------------------------------------------------------
## Run 588207  Cell selection  (Cell selection #8 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588207/"

## Running Cell selection [588207] [Cell selection #8 cell_sel] ()
echo '-> Running Cell selection [588207] [Cell selection #8 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_pca_1_pca_seurat_50D.sel_8 -f /data/asap2/users/1474/rzy6gj/metadata/588207/list_cols.json '


## ----------------------------------------------------------------
## Run 588208  Cell selection  (Cell selection #8 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588208/"

## Running Cell selection [588208] [Cell selection #8 cell_sel] ()
echo '-> Running Cell selection [588208] [Cell selection #8 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_pca_1_pca_seurat_50D.sel_8 -f /data/asap2/users/1474/rzy6gj/metadata/588208/list_cols.json '


## ----------------------------------------------------------------
## Run 588216  Clustering  (Clustering #1 seurat_sc)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/clustering/588216/"

## Running Clustering [588216] [Clustering #1 seurat_sc] (input_matrix:pca #1 nber_dims:50 resolution:0.8)
echo '-> Running Clustering [588216] [Clustering #1 seurat_sc] (input_matrix:pca #1 nber_dims:50 resolution:0.8)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588216 --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:v6 -c "sh -c 'Rscript --vanilla clustering.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom /matrix /col_attrs/_pca_1_pca_seurat_50D /col_attrs/_clust_1_seurat_sc /data/asap2/users/1474/rzy6gj/clustering/588216 50 0.8 1> /data/asap2/users/1474/rzy6gj/clustering/588216/exec.out 2> /data/asap2/users/1474/rzy6gj/clustering/588216/exec.err'"


## ----------------------------------------------------------------
## Run 588332  Cell selection  (Cell selection #10 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588332/"

## Running Cell selection [588332] [Cell selection #10 cell_sel] ()
echo '-> Running Cell selection [588332] [Cell selection #10 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_pca_1_pca_seurat_50D.sel_10 -f /data/asap2/users/1474/rzy6gj/metadata/588332/list_cols.json '


## ----------------------------------------------------------------
## Run 588677  Cell filtering  (Cell filtering #3 qc_plots)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_filtering/588677/"

## writing file $PROJECT_DIR/cell_filtering/588677/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/588677/discarded_cols.json'
docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "echo '{"discarded_cols":["2","3","4","7","11","14","16","20","23","24","28","29","35","37","38","43","46","47","54","58","60","61","62","64","72","73","74","77","80","81","83","84","85","89","93","95","103","104","106","107","108","109","112","115","120","129","135","137","138","139","146","147","150","152","154","158","161","165","168","170","172","173","174","180","184","185","187","190","191","192","193","195","198","207","213","214","216","217","220","222","225","226","228","229","232","233","235","236","240","248","249","253","254","255","256","260","261","265","274","276","280","282","290","301","303","307","311","315","318","325","334","340","342","346","352","359","360","361","362","363","364","367","371","374","376","385","386","390","393","394","395","399","400","402","404","408","412","422","425","430","433","436","437","439","440","443","444","446","449","454","458","464","468","471","472","475","477","478","479","481","482","486","487","491","494","496","498","502","503","509","510","511","513","523","527","531","534","535","537","539","540","547","548","554","558","560","561","564","570","571","572","573","574","577","579","582","584","585","586","587","597","598","605","612","613","615","617","626","634","635","647","650","653","656","657","658","659","660","661","662","663","664","665","667","669","674","679","682","684","685","686","688","689","691","692","697","700","701","704","705","706","709","713","724","726","727","733","741","743","745","748","749","750","755","771","778","780","781","782","785","795","800","803","804","805","809","811","813","815","819","822","824","832","836","840","844","845","847","850","854","856","861","866","872","878","879","881","882","887","889","891","894","899","901","904","907","910","911","913","920","922","923","928","929","930","934","939","942","943","944","946","949","952","954","955","956","958","960","961","962","965","970","975","979","980","981","982","984","985","989","994"]}' > $PROJECT_DIR/cell_filtering/588677/discarded_cols.json"

## writing file $PROJECT_DIR/cell_filtering/588677/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/588677/manually_discarded_cols.json'
docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "echo '{"manually_discarded_cols":[]}' > $PROJECT_DIR/cell_filtering/588677/manually_discarded_cols.json"

## Running Cell filtering [588677] [Cell filtering #3 qc_plots] (depth:1000 detected_genes:1000 protein_coding_content:80 mito_content:18 ribo_content:40 nber_manually_discarded_cols:0 input_matrix:parsing manual_selection:)
echo '-> Running Cell filtering [588677] [Cell filtering #3 qc_plots] (depth:1000 detected_genes:1000 protein_coding_content:80 mito_content:18 ribo_content:40 nber_manually_discarded_cols:0 input_matrix:parsing manual_selection:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588677 --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:v6 -c "sh -c 'java -jar /srv/ASAP.jar -T FilterCols -loom /data/asap2/users/1474/rzy6gj/parsing/output.loom -o /data/asap2/users/1474/rzy6gj/cell_filtering/588677 -col_indexes_file /data/asap2/users/1474/rzy6gj/cell_filtering/588677/discarded_cols.json  1> /data/asap2/users/1474/rzy6gj/cell_filtering/588677/exec.out 2> /data/asap2/users/1474/rzy6gj/cell_filtering/588677/exec.err'"


## ----------------------------------------------------------------
## Run 588678  Cell filtering  (Cell filtering #4 qc_plots)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_filtering/588678/"

## writing file $PROJECT_DIR/cell_filtering/588678/discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/588678/discarded_cols.json'
docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "echo '{"discarded_cols":["2","3","4","7","11","14","16","20","23","24","28","29","35","37","38","43","46","47","54","58","60","61","62","64","72","73","74","77","80","81","83","84","85","89","93","95","103","104","106","107","108","109","112","115","120","129","135","137","138","139","146","147","150","152","154","158","161","165","168","170","172","173","174","180","184","185","187","190","191","192","193","195","198","207","213","214","216","217","220","222","225","226","228","229","232","233","235","236","240","248","249","253","254","255","256","260","261","265","274","276","280","282","290","301","303","307","311","315","318","325","334","340","342","346","352","359","360","361","362","363","364","367","371","374","376","385","386","390","393","394","395","399","400","402","404","408","412","422","425","430","433","436","437","439","440","443","444","446","449","454","458","464","468","471","472","475","477","478","479","481","482","486","487","491","494","496","498","502","503","509","510","511","513","523","527","531","534","535","537","539","540","547","548","554","558","560","561","564","570","571","572","573","574","577","579","582","584","585","586","587","597","598","605","612","613","615","617","626","634","635","647","650","653","656","657","658","659","660","661","662","663","664","665","667","669","674","679","682","684","685","686","688","689","691","692","697","700","701","704","705","706","709","713","724","726","727","733","741","743","745","748","749","750","755","771","778","780","781","785","795","800","803","804","805","809","811","813","815","819","822","824","832","836","840","844","845","847","850","854","856","861","866","872","878","879","881","882","887","889","891","894","899","901","904","907","910","911","913","920","922","923","928","929","930","934","939","942","943","944","946","949","952","954","955","956","958","960","961","962","965","970","975","979","980","981","982","984","985","989","994"]}' > $PROJECT_DIR/cell_filtering/588678/discarded_cols.json"

## writing file $PROJECT_DIR/cell_filtering/588678/manually_discarded_cols.json
echo '-> writing file $PROJECT_DIR/cell_filtering/588678/manually_discarded_cols.json'
docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "echo '{"manually_discarded_cols":[]}' > $PROJECT_DIR/cell_filtering/588678/manually_discarded_cols.json"

## Running Cell filtering [588678] [Cell filtering #4 qc_plots] (depth:1000 detected_genes:1000 protein_coding_content:80 mito_content:20 ribo_content:36 nber_manually_discarded_cols:0 input_matrix:parsing manual_selection:)
echo '-> Running Cell filtering [588678] [Cell filtering #4 qc_plots] (depth:1000 detected_genes:1000 protein_coding_content:80 mito_content:20 ribo_content:36 nber_manually_discarded_cols:0 input_matrix:parsing manual_selection:)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588678 --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:v6 -c "sh -c 'java -jar /srv/ASAP.jar -T FilterCols -loom /data/asap2/users/1474/rzy6gj/parsing/output.loom -o /data/asap2/users/1474/rzy6gj/cell_filtering/588678 -col_indexes_file /data/asap2/users/1474/rzy6gj/cell_filtering/588678/discarded_cols.json  1> /data/asap2/users/1474/rzy6gj/cell_filtering/588678/exec.out 2> /data/asap2/users/1474/rzy6gj/cell_filtering/588678/exec.err'"


## ----------------------------------------------------------------
## Run 588680  t-SNE  (t-SNE #1 tsne_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/tsne/588680/"

## Running t-SNE [588680] [t-SNE #1 tsne_seurat] (input_matrix:pca #1 nber_pcs:50)
echo '-> Running t-SNE [588680] [t-SNE #1 tsne_seurat] (input_matrix:pca #1 nber_pcs:50)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588680 --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:v6 -c "sh -c 'Rscript --vanilla tsne.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom /matrix /col_attrs/_pca_1_pca_seurat_50D /col_attrs/_tsne_1_tsne_seurat_2D /data/asap2/users/1474/rzy6gj/tsne/588680 50 1> /data/asap2/users/1474/rzy6gj/tsne/588680/exec.out 2> /data/asap2/users/1474/rzy6gj/tsne/588680/exec.err'"


## ----------------------------------------------------------------
## Run 588681  UMAP  (UMAP #1 umap_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/umap/588681/"

## Running UMAP [588681] [UMAP #1 umap_seurat] (input_matrix:pca #1 nber_pcs:50)
echo '-> Running UMAP [588681] [UMAP #1 umap_seurat] (input_matrix:pca #1 nber_pcs:50)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588681 --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:v6 -c "sh -c 'Rscript --vanilla umap.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom /matrix /col_attrs/_pca_1_pca_seurat_50D /col_attrs/_umap_1_umap_seurat_2D /data/asap2/users/1474/rzy6gj/umap/588681 50 1> /data/asap2/users/1474/rzy6gj/umap/588681/exec.out 2> /data/asap2/users/1474/rzy6gj/umap/588681/exec.err'"


## ----------------------------------------------------------------
## Run 588682  Cell selection  (Cell selection #11 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588682/"

## Running Cell selection [588682] [Cell selection #11 cell_sel] ()
echo '-> Running Cell selection [588682] [Cell selection #11 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_11 -f /data/asap2/users/1474/rzy6gj/metadata/588682/list_cols.json '


## ----------------------------------------------------------------
## Run 588687  Module Score  (Module Score #1 seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/module_score/588687/"

## Running Module Score [588687] [Module Score #1 seurat] (input_matrix:normalization #1 geneset:cell_filtering #1 geneset_sel:1 n_bins:24 n_background_genes:100 seed:42)
echo '-> Running Module Score [588687] [Module Score #1 seurat] (input_matrix:normalization #1 geneset:cell_filtering #1 geneset_sel:1 n_bins:24 n_background_genes:100 seed:42)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588687 --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:v6 -c "sh -c 'java -jar /srv/ASAP.jar -T ModuleScore -o /data/asap2/users/1474/rzy6gj/module_score/588687/output.json -oAnnot /col_attrs/_mscore_1_seurat -metadata /row_attrs/_Chromosomes -sel 1 -m seurat -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -dataset /layers/norm_1_seurat -seed 42 -nBins 24 -nBackgroundGenes 100  1> /data/asap2/users/1474/rzy6gj/module_score/588687/exec.out 2> /data/asap2/users/1474/rzy6gj/module_score/588687/exec.err'"


## ----------------------------------------------------------------
## Run 588693  HVG  (HVG #2 vst)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/hvg/588693/"

## Running HVG [588693] [HVG #2 vst] (input_matrix:normalization #1 nber_features:500)
echo '-> Running HVG [588693] [HVG #2 vst] (input_matrix:normalization #1 nber_features:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588693 --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:v6 -c "sh -c 'Rscript --vanilla hvg.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom /matrix /layers/norm_1_seurat /row_attrs/hvg_2_vst /data/asap2/users/1474/rzy6gj/hvg/588693 vst 500 1> /data/asap2/users/1474/rzy6gj/hvg/588693/exec.out 2> /data/asap2/users/1474/rzy6gj/hvg/588693/exec.err'"


## ----------------------------------------------------------------
## Run 588695  Cell selection  (Cell selection #12 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588695/"

## Running Cell selection [588695] [Cell selection #12 cell_sel] ()
echo '-> Running Cell selection [588695] [Cell selection #12 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_12 -f /data/asap2/users/1474/rzy6gj/metadata/588695/list_cols.json '


## ----------------------------------------------------------------
## Run 588751  PCA  (PCA #2 pca_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/pca/588751/"

## Running PCA [588751] [PCA #2 pca_seurat] (input_matrix:scaling #1 variable_features_dataset:hvg #2 nber_dims:2)
echo '-> Running PCA [588751] [PCA #2 pca_seurat] (input_matrix:scaling #1 variable_features_dataset:hvg #2 nber_dims:2)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588751 --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:v6 -c "sh -c 'Rscript --vanilla pca.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom /matrix /layers/norm_1_seurat /layers/scaling_1_seurat /row_attrs/hvg_2_vst /col_attrs/_pca_2_pca_seurat_2D /data/asap2/users/1474/rzy6gj/pca/588751 2 1> /data/asap2/users/1474/rzy6gj/pca/588751/exec.out 2> /data/asap2/users/1474/rzy6gj/pca/588751/exec.err'"


## ----------------------------------------------------------------
## Run 588836  Normalization  (Normalization #2 seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/normalization/588836/"

## Running Normalization [588836] [Normalization #2 seurat] (input_matrix:cell_filtering #3)
echo '-> Running Normalization [588836] [Normalization #2 seurat] (input_matrix:cell_filtering #3)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588836 --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:v6 -c "sh -c 'Rscript --vanilla normalization.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588677/output.loom /matrix /layers/norm_2_seurat /data/asap2/users/1474/rzy6gj/normalization/588836 1> /data/asap2/users/1474/rzy6gj/normalization/588836/exec.out 2> /data/asap2/users/1474/rzy6gj/normalization/588836/exec.err'"


## ----------------------------------------------------------------
## Run 588838  Normalization  (Normalization #3 seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/normalization/588838/"

## Running Normalization [588838] [Normalization #3 seurat] (input_matrix:cell_filtering #4)
echo '-> Running Normalization [588838] [Normalization #3 seurat] (input_matrix:cell_filtering #4)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588838 --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:v6 -c "sh -c 'Rscript --vanilla normalization.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588678/output.loom /matrix /layers/norm_3_seurat /data/asap2/users/1474/rzy6gj/normalization/588838 1> /data/asap2/users/1474/rzy6gj/normalization/588838/exec.out 2> /data/asap2/users/1474/rzy6gj/normalization/588838/exec.err'"


## ----------------------------------------------------------------
## Run 588839  HVG  (HVG #3 vst)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/hvg/588839/"

## Running HVG [588839] [HVG #3 vst] (input_matrix:normalization #3 nber_features:3)
echo '-> Running HVG [588839] [HVG #3 vst] (input_matrix:normalization #3 nber_features:3)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588839 --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:v6 -c "sh -c 'Rscript --vanilla hvg.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588678/output.loom /matrix /layers/norm_3_seurat /row_attrs/hvg_3_vst /data/asap2/users/1474/rzy6gj/hvg/588839 vst 3 1> /data/asap2/users/1474/rzy6gj/hvg/588839/exec.out 2> /data/asap2/users/1474/rzy6gj/hvg/588839/exec.err'"


## ----------------------------------------------------------------
## Run 588840  Cell selection  (Cell selection #13 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588840/"

## Running Cell selection [588840] [Cell selection #13 cell_sel] ()
echo '-> Running Cell selection [588840] [Cell selection #13 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_pca_1_pca_seurat_50D.sel_13 -f /data/asap2/users/1474/rzy6gj/metadata/588840/list_cols.json '


## ----------------------------------------------------------------
## Run 588841  Cell selection  (Cell selection #14 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588841/"

## Running Cell selection [588841] [Cell selection #14 cell_sel] ()
echo '-> Running Cell selection [588841] [Cell selection #14 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_pca_1_pca_seurat_50D.sel_14 -f /data/asap2/users/1474/rzy6gj/metadata/588841/list_cols.json '


## ----------------------------------------------------------------
## Run 588842  Cell selection  (Cell selection #15 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588842/"

## Running Cell selection [588842] [Cell selection #15 cell_sel] ()
echo '-> Running Cell selection [588842] [Cell selection #15 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_15 -f /data/asap2/users/1474/rzy6gj/metadata/588842/list_cols.json '


## ----------------------------------------------------------------
## Run 588843  Cell selection  (Cell selection #16 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588843/"

## Running Cell selection [588843] [Cell selection #16 cell_sel] ()
echo '-> Running Cell selection [588843] [Cell selection #16 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_16 -f /data/asap2/users/1474/rzy6gj/metadata/588843/list_cols.json '


## ----------------------------------------------------------------
## Run 588844  Cell selection  (Cell selection #16 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588844/"

## Running Cell selection [588844] [Cell selection #16 cell_sel] ()
echo '-> Running Cell selection [588844] [Cell selection #16 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_16 -f /data/asap2/users/1474/rzy6gj/metadata/588844/list_cols.json '


## ----------------------------------------------------------------
## Run 588845  Cell selection  (Cell selection #18 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588845/"

## Running Cell selection [588845] [Cell selection #18 cell_sel] ()
echo '-> Running Cell selection [588845] [Cell selection #18 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_18 -f /data/asap2/users/1474/rzy6gj/metadata/588845/list_cols.json '


## ----------------------------------------------------------------
## Run 588847  Clustering  (Clustering #3 seurat_sc)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/clustering/588847/"

## Running Clustering [588847] [Clustering #3 seurat_sc] (input_matrix:pca #1 nber_dims:50 resolution:2)
echo '-> Running Clustering [588847] [Clustering #3 seurat_sc] (input_matrix:pca #1 nber_dims:50 resolution:2)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588847 --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:v6 -c "sh -c 'Rscript --vanilla clustering.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom /matrix /col_attrs/_pca_1_pca_seurat_50D /col_attrs/_clust_3_seurat_sc /data/asap2/users/1474/rzy6gj/clustering/588847 50 2 1> /data/asap2/users/1474/rzy6gj/clustering/588847/exec.out 2> /data/asap2/users/1474/rzy6gj/clustering/588847/exec.err'"


## ----------------------------------------------------------------
## Run 588849  Cell selection  (Cell selection #19 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588849/"

## Running Cell selection [588849] [Cell selection #19 cell_sel] ()
echo '-> Running Cell selection [588849] [Cell selection #19 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_19 -f /data/asap2/users/1474/rzy6gj/metadata/588849/list_cols.json '


## ----------------------------------------------------------------
## Run 588850  Cell selection  (Cell selection #20 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588850/"

## Running Cell selection [588850] [Cell selection #20 cell_sel] ()
echo '-> Running Cell selection [588850] [Cell selection #20 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_20 -f /data/asap2/users/1474/rzy6gj/metadata/588850/list_cols.json '


## ----------------------------------------------------------------
## Run 588853  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:v6 -c "mkdir -p $PROJECT_DIR/markers/588853/"

## Running Find markers [588853] [Find markers #1 asap_markers] (input_matrix:cell_filtering #1)
echo '-> Running Find markers [588853] [Find markers #1 asap_markers] (input_matrix:cell_filtering #1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588853 --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:v6 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -o /data/asap2/users/1474/rzy6gj/markers/588853 --iAnnot /col_attrs/_clust_3_seurat_sc --id 4558044 --is_count_table true  1> /data/asap2/users/1474/rzy6gj/markers/588853/exec.out 2> /data/asap2/users/1474/rzy6gj/markers/588853/exec.err'"


## ----------------------------------------------------------------
## Run 588866  Cell selection  (Cell selection #21 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588866/"

## Running Cell selection [588866] [Cell selection #21 cell_sel] ()
echo '-> Running Cell selection [588866] [Cell selection #21 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_21 -f /data/asap2/users/1474/rzy6gj/metadata/588866/list_cols.json '


## ----------------------------------------------------------------
## Run 588867  Cell selection  (Cell selection #22 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/588867/"

## Running Cell selection [588867] [Cell selection #22 cell_sel] ()
echo '-> Running Cell selection [588867] [Cell selection #22 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_22 -f /data/asap2/users/1474/rzy6gj/metadata/588867/list_cols.json '


## ----------------------------------------------------------------
## Run 588869  Differential expression  (Differential expression #1 wilcox_asap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/de/588869/"

## Running Differential expression [588869] [Differential expression #1 wilcox_asap] (input_matrix:normalization #1 groups:clustering #3 group_ref:1 group_comp:7)
echo '-> Running Differential expression [588869] [Differential expression #1 wilcox_asap] (input_matrix:normalization #1 groups:clustering #3 group_ref:1 group_comp:7)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588869 --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:v6 -c "sh -c 'java -jar /srv/ASAP.jar -T DifferentialExpression -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -o /data/asap2/users/1474/rzy6gj/de/588869 -m wilcox_asap -iAnnot /layers/norm_1_seurat -oAnnot /row_attrs/_de_1_wilcox_asap -gAnnot /col_attrs/_clust_3_seurat_sc -g1 1 -g2 7 --is_count_table false  1> /data/asap2/users/1474/rzy6gj/de/588869/exec.out 2> /data/asap2/users/1474/rzy6gj/de/588869/exec.err'"


## ----------------------------------------------------------------
## Run 588874  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:v6 -c "mkdir -p $PROJECT_DIR/ge/588874/"

## Running Gene Enrichment [588874] [Gene Enrichment #1 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [588874] [Gene Enrichment #1 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588874 --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:v6 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -m fet -f /data/asap2/users/1474/rzy6gj/tmp/1474_588869_2_0.05_filtered_ids.json -o /data/asap2/users/1474/rzy6gj/ge/588874/output.json -max 500 -min 15 -adj fdr -geneset 3152 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6  1> /data/asap2/users/1474/rzy6gj/ge/588874/exec.out 2> /data/asap2/users/1474/rzy6gj/ge/588874/exec.err'"


## ----------------------------------------------------------------
## Run 588875  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:v6 -c "mkdir -p $PROJECT_DIR/ge/588875/"

## Running Gene Enrichment [588875] [Gene Enrichment #2 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)
echo '-> Running Gene Enrichment [588875] [Gene Enrichment #2 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_588875 --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:v6 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -m fet -f /data/asap2/users/1474/rzy6gj/tmp/1474_588869_2_0.05_filtered_ids.json -o /data/asap2/users/1474/rzy6gj/ge/588875/output.json -max 500 -min 15 -adj fdr -geneset 2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6  1> /data/asap2/users/1474/rzy6gj/ge/588875/exec.out 2> /data/asap2/users/1474/rzy6gj/ge/588875/exec.err'"


## ----------------------------------------------------------------
## Run 588905  Clustering  (Clustering #4 seurat_sc)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/clustering/588905/"

## Running Clustering [588905] [Clustering #4 seurat_sc] (input_matrix:pca #1 nber_dims:50 resolution:3.5)
echo '-> Running Clustering [588905] [Clustering #4 seurat_sc] (input_matrix:pca #1 nber_dims:50 resolution:3.5)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_588905 --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:v6 -c "sh -c 'Rscript --vanilla clustering.asap.3.R  /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom /matrix /col_attrs/_pca_1_pca_seurat_50D /col_attrs/_clust_4_seurat_sc /data/asap2/users/1474/rzy6gj/clustering/588905 50 3.5 1> /data/asap2/users/1474/rzy6gj/clustering/588905/exec.out 2> /data/asap2/users/1474/rzy6gj/clustering/588905/exec.err'"


## ----------------------------------------------------------------
## Run 589346  Cell selection  (Cell selection #23 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/589346/"

## Running Cell selection [589346] [Cell selection #23 cell_sel] ()
echo '-> Running Cell selection [589346] [Cell selection #23 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_23 -f /data/asap2/users/1474/rzy6gj/metadata/589346/list_cols.json '


## ----------------------------------------------------------------
## Run 589347  Cell selection  (Cell selection #24 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/589347/"

## Running Cell selection [589347] [Cell selection #24 cell_sel] ()
echo '-> Running Cell selection [589347] [Cell selection #24 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_24 -f /data/asap2/users/1474/rzy6gj/metadata/589347/list_cols.json '


## ----------------------------------------------------------------
## Run 589348  Cell selection  (Cell selection #25 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/589348/"

## Running Cell selection [589348] [Cell selection #25 cell_sel] ()
echo '-> Running Cell selection [589348] [Cell selection #25 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_25 -f /data/asap2/users/1474/rzy6gj/metadata/589348/list_cols.json '


## ----------------------------------------------------------------
## Run 589349  Cell selection  (Cell selection #26 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/589349/"

## Running Cell selection [589349] [Cell selection #26 cell_sel] ()
echo '-> Running Cell selection [589349] [Cell selection #26 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_26 -f /data/asap2/users/1474/rzy6gj/metadata/589349/list_cols.json '


## ----------------------------------------------------------------
## Run 589350  Differential expression  (Differential expression #2 wilcox_asap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/de/589350/"

## Running Differential expression [589350] [Differential expression #2 wilcox_asap] (input_matrix:normalization #1 groups:cell_selection #26 group_ref:0 group_comp:1)
echo '-> Running Differential expression [589350] [Differential expression #2 wilcox_asap] (input_matrix:normalization #1 groups:cell_selection #26 group_ref:0 group_comp:1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_589350 --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:v6 -c "sh -c 'java -jar /srv/ASAP.jar -T DifferentialExpression -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -o /data/asap2/users/1474/rzy6gj/de/589350 -m wilcox_asap -iAnnot /layers/norm_1_seurat -oAnnot /row_attrs/_de_2_wilcox_asap -gAnnot /col_attrs/_umap_1_umap_seurat_2D.sel_26 -g1 0 -g2 1 --is_count_table false  1> /data/asap2/users/1474/rzy6gj/de/589350/exec.out 2> /data/asap2/users/1474/rzy6gj/de/589350/exec.err'"


## ----------------------------------------------------------------
## Run 589410  Differential expression  (Differential expression #3 wilcox_asap)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/de/589410/"

## Running Differential expression [589410] [Differential expression #3 wilcox_asap] (input_matrix:normalization #1 groups:clustering #3 group_ref:7 group_comp:1)
echo '-> Running Differential expression [589410] [Differential expression #3 wilcox_asap] (input_matrix:normalization #1 groups:clustering #3 group_ref:7 group_comp:1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_589410 --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:v6 -c "sh -c 'java -jar /srv/ASAP.jar -T DifferentialExpression -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -o /data/asap2/users/1474/rzy6gj/de/589410 -m wilcox_asap -iAnnot /layers/norm_1_seurat -oAnnot /row_attrs/_de_3_wilcox_asap -gAnnot /col_attrs/_clust_3_seurat_sc -g1 7 -g2 1 --is_count_table false  1> /data/asap2/users/1474/rzy6gj/de/589410/exec.out 2> /data/asap2/users/1474/rzy6gj/de/589410/exec.err'"


## ----------------------------------------------------------------
## Run 589421  Cell selection  (Cell selection #27 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/589421/"

## Running Cell selection [589421] [Cell selection #27 cell_sel] ()
echo '-> Running Cell selection [589421] [Cell selection #27 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_27 -f /data/asap2/users/1474/rzy6gj/metadata/589421/list_cols.json '


## ----------------------------------------------------------------
## Run 589422  Cell selection  (Cell selection #28 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/589422/"

## Running Cell selection [589422] [Cell selection #28 cell_sel] ()
echo '-> Running Cell selection [589422] [Cell selection #28 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_28 -f /data/asap2/users/1474/rzy6gj/metadata/589422/list_cols.json '


## ----------------------------------------------------------------
## Run 589423  Cell selection  (Cell selection #29 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/589423/"

## Running Cell selection [589423] [Cell selection #29 cell_sel] ()
echo '-> Running Cell selection [589423] [Cell selection #29 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_29 -f /data/asap2/users/1474/rzy6gj/metadata/589423/list_cols.json '


## ----------------------------------------------------------------
## Run 589424  Cell selection  (Cell selection #29 cell_sel)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v6 -c "mkdir -p $PROJECT_DIR/cell_selection/589424/"

## Running Cell selection [589424] [Cell selection #29 cell_sel] ()
echo '-> Running Cell selection [589424] [Cell selection #29 cell_sel] ()'

## Command
sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -meta /col_attrs/_umap_1_umap_seurat_2D.sel_29 -f /data/asap2/users/1474/rzy6gj/metadata/589424/list_cols.json '


## ----------------------------------------------------------------
## Run 589425  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:v6 -c "mkdir -p $PROJECT_DIR/de/589425/"

## Running Differential expression [589425] [Differential expression #4 wilcox_asap] (input_matrix:normalization #1 groups:cell_selection #29 group_ref:0 group_comp:1)
echo '-> Running Differential expression [589425] [Differential expression #4 wilcox_asap] (input_matrix:normalization #1 groups:cell_selection #29 group_ref:0 group_comp:1)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_589425 --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:v6 -c "sh -c 'java -jar /srv/ASAP.jar -T DifferentialExpression -loom /data/asap2/users/1474/rzy6gj/cell_filtering/588195/output.loom -o /data/asap2/users/1474/rzy6gj/de/589425 -m wilcox_asap -iAnnot /layers/norm_1_seurat -oAnnot /row_attrs/_de_4_wilcox_asap -gAnnot /col_attrs/_umap_1_umap_seurat_2D.sel_29 -g1 0 -g2 1 --is_count_table false  1> /data/asap2/users/1474/rzy6gj/de/589425/exec.out 2> /data/asap2/users/1474/rzy6gj/de/589425/exec.err'"