## This script contains all commands executed in the PROJECT n8dmko and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT n8dmko / ASAP133**********************'
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/n8dmko
## Pull Docker images (must run before any docker run in this script)

docker pull fabdavid/asap_run:v8

## Host LOOM staging directory (inside Docker volume)
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -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_v8; then echo 'Create database asap_data_v8'; echo '$PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v8'; $PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v8; echo 'wget -qO - https://asap.epfl.ch/dumps/asap_data_v8.sql.gz | gunzip | grep -v \'AS integer\' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v8'; wget -qO - https://asap.epfl.ch/dumps/asap_data_v8.sql.gz | gunzip | grep -v 'AS integer' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v8; fi

## Project directory on the shared volume
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -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:v8 -c "mkdir -p $PROJECT_DIR/parsing/ && mkdir -p $PROJECT_DIR/heatmap/ && mkdir -p $PROJECT_DIR/cell_selection/ && mkdir -p $PROJECT_DIR/markers/ && mkdir -p $PROJECT_DIR/export_h5ad/"

## 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:v8 -c "wget -qO $PROJECT_DIR/parsing/output.loom 'https://asap.epfl.ch/projects/n8dmko/get_file?filename=parsing/output.loom'"

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


## ----------------------------------------------------------------
## Run 834223  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:v8 -c "mkdir -p $PROJECT_DIR/cell_selection/834223/"

## Running Cell selection [834223] [Cell selection #1 cell_sel] ()
echo '-> Running Cell selection [834223] [Cell selection #1 cell_sel] ()'

## Command
sh -c 'java -jar /srv/asap_run_new/java/bin//ASAP.jar -T CreateCellSelection -loom $PROJECT_DIR/parsing/output.loom -meta /col_attrs/X_tsne.sel_1 -f $PROJECT_DIR/metadata/834223/selected_cells.json '


## ----------------------------------------------------------------
## Run 834224  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:v8 -c "mkdir -p $PROJECT_DIR/cell_selection/834224/"

## Running Cell selection [834224] [Cell selection #2 cell_sel] ()
echo '-> Running Cell selection [834224] [Cell selection #2 cell_sel] ()'

## Command
sh -c 'java -jar /srv/asap_run_new/java/bin//ASAP.jar -T CreateCellSelection -loom $PROJECT_DIR/parsing/output.loom -meta /col_attrs/X_tsne.sel_2 -f $PROJECT_DIR/metadata/834224/selected_cells.json '


## ----------------------------------------------------------------
## Run 834295  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:v8 -c "mkdir -p $PROJECT_DIR/markers/834295/"

## Running Find markers [834295] [Find markers #1 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834295] [Find markers #1 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834295 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834295 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834295/exec.out 2> $PROJECT_DIR/markers/834295/exec.err'"


## ----------------------------------------------------------------
## Run 834297  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:v8 -c "mkdir -p $PROJECT_DIR/cell_selection/834297/"

## Running Cell selection [834297] [Cell selection #3 cell_sel] ()
echo '-> Running Cell selection [834297] [Cell selection #3 cell_sel] ()'

## Command
sh -c 'h5py write_cell_selection -loom $PROJECT_DIR/parsing/output.loom -meta /col_attrs/X_tsne.sel_3 -f $PROJECT_DIR/metadata/834297/selected_cells.json '


## ----------------------------------------------------------------
## Run 834337  Find markers  (Find markers #2 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834337/"

## Running Find markers [834337] [Find markers #2 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834337] [Find markers #2 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834337 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834337 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834337/exec.out 2> $PROJECT_DIR/markers/834337/exec.err'"


## ----------------------------------------------------------------
## Run 834338  Find markers  (Find markers #3 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834338/"

## Running Find markers [834338] [Find markers #3 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834338] [Find markers #3 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834338 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834338 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834338/exec.out 2> $PROJECT_DIR/markers/834338/exec.err'"


## ----------------------------------------------------------------
## Run 834341  Find markers  (Find markers #4 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834341/"

## Running Find markers [834341] [Find markers #4 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834341] [Find markers #4 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834341 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834341 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834341/exec.out 2> $PROJECT_DIR/markers/834341/exec.err'"


## ----------------------------------------------------------------
## Run 834343  Find markers  (Find markers #5 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834343/"

## Running Find markers [834343] [Find markers #5 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834343] [Find markers #5 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834343 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834343 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834343/exec.out 2> $PROJECT_DIR/markers/834343/exec.err'"


## ----------------------------------------------------------------
## Run 834344  Find markers  (Find markers #6 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834344/"

## Running Find markers [834344] [Find markers #6 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834344] [Find markers #6 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834344 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834344 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834344/exec.out 2> $PROJECT_DIR/markers/834344/exec.err'"


## ----------------------------------------------------------------
## Run 834345  Find markers  (Find markers #7 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834345/"

## Running Find markers [834345] [Find markers #7 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834345] [Find markers #7 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834345 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834345 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834345/exec.out 2> $PROJECT_DIR/markers/834345/exec.err'"


## ----------------------------------------------------------------
## Run 834346  Find markers  (Find markers #8 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834346/"

## Running Find markers [834346] [Find markers #8 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834346] [Find markers #8 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834346 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834346 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834346/exec.out 2> $PROJECT_DIR/markers/834346/exec.err'"


## ----------------------------------------------------------------
## Run 834347  Find markers  (Find markers #9 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834347/"

## Running Find markers [834347] [Find markers #9 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834347] [Find markers #9 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834347 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834347 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834347/exec.out 2> $PROJECT_DIR/markers/834347/exec.err'"


## ----------------------------------------------------------------
## Run 834348  Find markers  (Find markers #10 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834348/"

## Running Find markers [834348] [Find markers #10 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834348] [Find markers #10 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834348 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834348 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834348/exec.out 2> $PROJECT_DIR/markers/834348/exec.err'"


## ----------------------------------------------------------------
## Run 834349  Find markers  (Find markers #11 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834349/"

## Running Find markers [834349] [Find markers #11 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834349] [Find markers #11 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834349 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834349 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834349/exec.out 2> $PROJECT_DIR/markers/834349/exec.err'"


## ----------------------------------------------------------------
## Run 834350  Find markers  (Find markers #12 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834350/"

## Running Find markers [834350] [Find markers #12 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834350] [Find markers #12 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834350 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834350 --method wilcoxon --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv  1> $PROJECT_DIR/markers/834350/exec.out 2> $PROJECT_DIR/markers/834350/exec.err'"


## ----------------------------------------------------------------
## Run 834351  Find markers  (Find markers #13 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/markers/834351/"

## Running Find markers [834351] [Find markers #13 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [834351] [Find markers #13 asap_markers] (input_matrix:parsing)'

## Command
docker run  --name asap_834351 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python de_approx.v8.py -f $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/markers/834351 --method t_test_approx --input-dataset /matrix --group-dataset /col_attrs/cell_type --is-count true --write-tsv --preview-max-cells 10000  1> $PROJECT_DIR/markers/834351/exec.out 2> $PROJECT_DIR/markers/834351/exec.err'"


## ----------------------------------------------------------------
## Run 834352  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:v8 -c "mkdir -p $PROJECT_DIR/cell_selection/834352/"

## Running Cell selection [834352] [Cell selection #4 cell_sel] ()
echo '-> Running Cell selection [834352] [Cell selection #4 cell_sel] ()'

## Command
sh -c 'h5py write_cell_selection -loom $PROJECT_DIR/parsing/output.loom -meta /col_attrs/X_tsne.sel_4 -f $PROJECT_DIR/metadata/834352/selected_cells.json '


## ----------------------------------------------------------------
## Run 834353  Heatmap  (Heatmap #1)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/heatmap/834353/"

## Running Heatmap [834353] [Heatmap #1] (input_matrix:parsing Cells/samples metadata:[] Gene set collection:GO Biological Processes Gene set:GO:0019730 antimicrobial humoral response Grouping metadata:[])
echo '-> Running Heatmap [834353] [Heatmap #1] (input_matrix:parsing Cells/samples metadata:[] Gene set collection:GO Biological Processes Gene set:GO:0019730 antimicrobial humoral response Grouping metadata:[])'

## Command
docker run  --name asap_834353 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python3.12 heatmap.v8.py -f $PROJECT_DIR/parsing/output.loom --input_meta /matrix -o $PROJECT_DIR/heatmap/834353 --config $PROJECT_DIR/heatmap/834353/heatmap_config.json  1> $PROJECT_DIR/heatmap/834353/exec.out 2> $PROJECT_DIR/heatmap/834353/exec.err'"


## ----------------------------------------------------------------
## Run 834354  Heatmap  (Heatmap #2)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/heatmap/834354/"

## Running Heatmap [834354] [Heatmap #2] (input_matrix:parsing cells_metadata:cell_selection #4 Category filter:["1"] Gene set collection:GO Biological Processes Gene set:GO:0022610 biological adhesion Grouping metadata:[])
echo '-> Running Heatmap [834354] [Heatmap #2] (input_matrix:parsing cells_metadata:cell_selection #4 Category filter:["1"] Gene set collection:GO Biological Processes Gene set:GO:0022610 biological adhesion Grouping metadata:[])'

## Command
docker run  --name asap_834354 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python3.12 heatmap.v8.py -f $PROJECT_DIR/parsing/output.loom --input_meta /matrix -o $PROJECT_DIR/heatmap/834354 --config $PROJECT_DIR/heatmap/834354/heatmap_config.json  1> $PROJECT_DIR/heatmap/834354/exec.out 2> $PROJECT_DIR/heatmap/834354/exec.err'"


## ----------------------------------------------------------------
## Run 834355  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:v8 -c "mkdir -p $PROJECT_DIR/cell_selection/834355/"

## Running Cell selection [834355] [Cell selection #5 cell_sel] ()
echo '-> Running Cell selection [834355] [Cell selection #5 cell_sel] ()'

## Command
sh -c 'h5py write_cell_selection -loom $PROJECT_DIR/parsing/output.loom -meta /col_attrs/X_tsne.sel_5 -f $PROJECT_DIR/metadata/834355/selected_cells.json '


## ----------------------------------------------------------------
## Run 834356  Export H5AD  (Export H5AD #1 loom_to_h5ad)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/export_h5ad/834356/"

## Running Export H5AD [834356] [Export H5AD #1 loom_to_h5ad] (Input Loom path:parsing/output.loom Input Loom absolute path:/data/asap/users/6/n8dmko/parsing/output.loom Output H5AD absolute path:/data/asap/users/6/n8dmko/parsing/output.h5ad)
echo '-> Running Export H5AD [834356] [Export H5AD #1 loom_to_h5ad] (Input Loom path:parsing/output.loom Input Loom absolute path:/data/asap/users/6/n8dmko/parsing/output.loom Output H5AD absolute path:/data/asap/users/6/n8dmko/parsing/output.h5ad)'

## Command
docker run  --name asap_834356 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python loom_to_h5ad.v8.py -i $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/parsing/output.h5ad -d $PROJECT_DIR/export_h5ad/834356  1> $PROJECT_DIR/export_h5ad/834356/exec.out 2> $PROJECT_DIR/export_h5ad/834356/exec.err'"


## ----------------------------------------------------------------
## Run 834357  Export H5AD  (Export H5AD #2 loom_to_h5ad)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v8 -c "mkdir -p $PROJECT_DIR/export_h5ad/834357/"

## Running Export H5AD [834357] [Export H5AD #2 loom_to_h5ad] (Input Loom path:parsing/output.loom Input Loom absolute path:/data/asap/users/6/n8dmko/parsing/output.loom Output H5AD absolute path:/data/asap/users/6/n8dmko/parsing/output.h5ad)
echo '-> Running Export H5AD [834357] [Export H5AD #2 loom_to_h5ad] (Input Loom path:parsing/output.loom Input Loom absolute path:/data/asap/users/6/n8dmko/parsing/output.loom Output H5AD absolute path:/data/asap/users/6/n8dmko/parsing/output.h5ad)'

## Command
docker run  --name asap_834357 --network=asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap:/data/asap -v /mnt/asap_data/ensembl:/mnt/asap_data/ensembl:ro -e ENSEMBL_DATA_DIR=/mnt/asap_data/ensembl --env-file /data/asap/.env_asap_run  fabdavid/asap_run:v8 -c "sh -c 'python loom_to_h5ad.v8.py -i $PROJECT_DIR/parsing/output.loom -o $PROJECT_DIR/parsing/output.h5ad -d $PROJECT_DIR/export_h5ad/834357  1> $PROJECT_DIR/export_h5ad/834357/exec.out 2> $PROJECT_DIR/export_h5ad/834357/exec.err'"