I'm trying to write an xml wrapper for a script which generates an html file ("report.html") in an output directory specified with the -o parameter. The script correctly executes but when I click on the "information" icon, the command line shows me the path for "$html_file.files_path" yet the directory does not exist. Can anyone give me any suggestions? Relevant lines of xml are below:
<command>python script.py -o "$html_file.files_path" </command>
<outputs>
<data name="html_file" format="html" from_work_dir="report.html" label="Output (HTML) on ${on_string}"/>
</outputs>
when I look at the command line, the output directory is specified as:
/remote/home/user/galaxy/database/job_working_directory/000/576/dataset_687_files
but when I search for the output file, it is found here:
/remote/home/user/galaxy/database/files/000/dataset_687_files/
Thanks!
This appears to be the same as this issue:
Galaxy Passing An Incorrect Directory To A Script...
However, if I use the "extra_files_path" i still get the same result in that the data is placed in "files/000/dataset_xxx_files/" rather than "job_working_directory/000/XXX/dataset_xxx_files"
ok - so that old difference between extra_files_path and files_path has been resolved - that's good!
At completion of a job, galaxy moves things from the transient job working directory to permanent storage as you've noticed. That means tools can happily spew out temporary messy stuff to that transient working directory but at the end, only the tool code specified and user-ready outputs are available for viewing in a history. I'm not sure what you were expecting or why this is a problem?
Sorry, i just realized I switched the directory names, I've since changed the comment..
In the <command> I'm passing the temporary directory, the results get copied to the final spot. However, the html file I receive from the galaxy interface is empty (the file report.html).
The instructions for doing this seem to suggest that I'm doing everything correctly:
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
Any suggestions would be greatly appreciated
Maybe this is a bug, but it works fine if I add this to the <command>:
; cp $html_file.files_path/report.html $html_file