Question: Custom tool creates output in a directory -- how to make the user interface aware of it?
gravatar for LF
3.5 years ago by
United States
LF10 wrote:

Hi all,

I have a perl script I am trying to integrate into a galaxy server. The script generates a variable number of output files and saves them in an output directory.

I am wondering how to make the user interface of the galaxy server aware of this output.

I put some debug statements into the perl script and it outputs where it saves the newly-generated files. For example:

Set up output file: /mnt/bioinfohd1/jmac/galaxy-userdata/database/job_working_directory/001/1494/debarcode_output/Sample_A.01.TCCCTTGTCTCC.R1.fastq
Set up output file: /mnt/bioinfohd1/jmac/galaxy-userdata/database/job_working_directory/001/1494/debarcode_output/Sample_B.02.ACGAGACTGATT.R1.fastq

However, after the script runs to completion, the data does not exist in this location, and it also doesn't show up anywhere in the right-hand side list of files.

How can I make Galaxy aware of the output files? Do I have to move these files to a new location right after running the script (i.e. in the tool's XML file in the <command> tags)?

Thanks for any advice!

ADD COMMENTlink modified 3.5 years ago by Jennifer Hillman Jackson25k • written 3.5 years ago by LF10
gravatar for Jennifer Hillman Jackson
3.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Please see #4 in this development tutorial: AddToolTutorial

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3.5 years ago by Jennifer Hillman Jackson25k

Thanks for the suggestion!

I actually already have the tool running in galaxy! The output I posted above is debugging messages that the tool prints to stdout. The only part I'm stuck on is how to make the output available to the galaxy user. It looks like the tool runs to completion just fine, but I can't find the data its generates (the file paths that the debugging messages report do not exist after the program runs to completion).

ADD REPLYlink written 3.5 years ago by LF10
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