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BioWardrobe Airflow Advanced Analysis

Requirements

1 To generate outputs for DeSeq the following programs should be installed

  • R
    • data.table library

How to init advanced analysis

Run on behalf of the user who has permissions to read BioWardrobe configuration file

biowardrobe-advanced-init

Use -c to use custom configuration file.

It will do the following steps:

  • read BioWardrobe configuration from /etc/wardrobe/wardrobe file to get access to BioWardobe's DB
  • generate missing output files and update params field in DB
  • apply patches from sql_patches folder
    • add params column to ems.atdp
    • add params column to ems.genelist

It's safe to run biowardrobe-advanced-init more then one time if necessarry.

How make it run from php scripts

  1. To be able to run DeSeq

    • copy biowardrobe_airflow_advanced/scripts/run_deseq.sh to the folder with DESeqPrjRun.php as DESeqPrjRun.sh
    • update DESeqPrjRun.php with the following lines 
      $CMD_CWL = "./DESeqPrjRun.sh " . $tablepairs[$i]['t1'] . " " . $tablepairs[$i]['t2'] . " $rtypeid '$projectid' '$RNAME' $UUID";
exec($CMD_CWL);

    For more details refer to the /wardrobe/src.new/EMS/ems/data/DESeqPrjRun.php

  2. To be able to build Heatmap

    • copy biowardrobe_airflow_advanced/scripts/run_heatmap.sh to the folder with ATDPPrjRun.php as ATDPPrjRun.sh
    • update ATDPPrjRun.php with the following lines 
      $CMD_CWL = "./ATDPPrjRun.sh" . " " . $atdp[$i]->tableD . " " . $atdp[$i]->tableL . " '" . $atdp[$i]->pltname . "' " . $UUID;
exec($CMD_CWL);

    For more details refer to the /wardrobe/src.new/EMS/ems/data/ATDPPrjRun.php

  3. To be able to display Heatmap

    • copy biowardrobe_airflow_advanced/scripts/load_heatmap.py to the folder with ATDPHeatA.php as ATDPHeatA.py
    • update ATDPHeatA.php with the following lines 
      $resutls_folder = $settings->settings['wardrobe']['value'] . '/' . $settings->settings['advanced']['value'] . '/' . $uid;
if (file_exists($resutls_folder))
  $command = "python3.6 ./ATDPHeatA.py -f " . $resutls_folder;
else
  $command = "{$BIN}/atdp --avd_guid=\"{$uid}\" -log=\"{$TMP}/atdpheat.log\" --avd_heat_window=\"400\" -sam_twicechr=\"chrX chrY\" -sam_ignorechr=\"chrM\" -avd_window=4000 -avd_bsmooth=40 -avd_smooth=200 ";

    For more details refer to the /wardrobe/src.new/EMS/ems/data/ATDPHeatA.php

  4. To run PCA

    • copy biowardrobe_airflow_advanced/scripts/run_pca.sh to the folder with RPrjRun.php as RPrjRun.sh
    • update RPrjRun.php with the following lines 
      //$exec_result = shell_exec($command);   <----- THIS IS THE OLD STRING

// Update to run PCA with CWL
if ($rscriptid=="PCA00000-0000-0000-0000-000000000001") {
    $CMD_CWL = "/wardrobe/src.new/EMS/ems/data/RPrjRun.sh" . " " . $d->id . " " . $rargs;
    exec($CMD_CWL);
} else {
    $exec_result = shell_exec($command);
}
    • make sure that you set the absolute path to the RPrjRun.sh, because current directory is changed within RPrjRun.php
    • make sure that PCA00000-0000-0000-0000-000000000001 corresponds to the correct id in ems.advanced_r