Question: Having trouble passing outputs through a wrapper
gravatar for kramdi.a
4.5 years ago by
kramdi.a40 wrote:


I am trying to integrated a developed tool into Galaxy. I have to write a wrapper (I chose python) because the line command of my tool does not specify the outputs.

-A few remarks:

*I run a single user Galaxy instance (default install) 

* my tool generates 4 outputs + 1 log file. You can see below the command line tag and the I use. 

The job is not going right, here's what's happening after executing the tool:

- I can see 5 dataset_XXX getting generated in the default database/file/000, however, I noticed there was a discordance in the the number (_XXX) attached compared to what I see in Galaxy History, I don't know why.

- The task completes with an error generated from the as if the process called (my tool) failed, but when I go look into the in database/file/000, all the generated files are empty except for the logging file which looks as if the tool completed the task...Where did the tool's outputs go ?

The problem seems to be in the capture of outputs by Galaxy. I am actually having a hard time understanding the communication between the tool and Galaxy when it comes to outputs passed through a wrapper.

Here's my, 

Any remarques would be appreciated.

Thank you 



<command interpreter="python"> '$input_chip_file' '$input_control_file' '$config_file' '$project_name' '$output_peaks_file' '$output_regions_file' '$output_density_file' '$output_proba_file' '$log_report'</command>


#!/usr/bin/env python

import sys, subprocess, tempfile, os, shutil


if __name__ == "__main__":


  input_chip_file = sys.argv[1]

  input_control_file = sys.argv[2]

  config_file = sys.argv[3]

  project_name = sys.argv[4]

  output_peaks_file = sys.argv[5]

  output_regions_file = sys.argv[6]

  output_density_file = sys.argv[7]

  output_proba_file = sys.argv[8]

  log_report = sys.argv[9]


  #create tmp dir:




       proc=subprocess.Popen(args= "%s %s > %s" % (TOOL_BINARY, " ".join([input_chip_file, input_control_file,   config_file , project_name]), log_report ), shell=True, cwd=tmp_dir)

       #check process

       returncode = proc.wait()

       if returncode :

       raise Exception

       #deal with outputs

       shutil.move( os.path.join(tmp_dir, "%s_peaks.bed" % project_name) ,output_peaks_file )

       shutil.move( os.path.join( tmp_dir, "%s_regions.bed" % project_name ) ,output_regions_file )

       shutil.move( os.path.join( tmp_dir, "%s_density.bed" % project_name ) ,output_density_file )

       shutil.move( os.path.join( tmp_dir, "%s_proba.bed" % project_name ) ,output_proba_file )

       shutil.move( os.path.join( tmp_dir, "%s.bed" % project_name ) ,output_density_file )

  #handle Exception

  except Exception:

       sys.stderr.write ("Error while runing TOOL\n")


       raise Exception 

  shutil.rmtree(tmp_dir) #clean up working dir


outputs galaxy python wrapper • 1.5k views
ADD COMMENTlink modified 3.6 years ago by rlee0350 • written 4.5 years ago by kramdi.a40

Can you please give us a link to your Galaxy XML wrapper.

ADD REPLYlink written 4.5 years ago by Bjoern Gruening5.1k
gravatar for kramdi.a
4.5 years ago by
kramdi.a40 wrote:

I actually found what was wrong this morning, a silly inadvertence error when I copy the outputs. As you can see there are 5 shutil.move() calls when I only need to move 4 files (no more copy/paste..). Now the job completes successfully and I have access to all outputs in the history panel. 

However, the discordance is still there, it's not hurting the job, but I'm wondering what happened. Maybe because I deleted some of the older empty datasets ?

in /../file/000 I see : dataset_401/402/403/404/405 , in the history panel 400/401/402/403/404 and they all map. 

ADD COMMENTlink written 4.5 years ago by kramdi.a40
gravatar for rlee03
3.6 years ago by
United States
rlee0350 wrote:

How would you know which sys.argv[1] is mapped to   input_chip_file  etc...

ADD COMMENTlink written 3.6 years ago by rlee0350
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