Closed neoformit closed 1 year ago
Can you test this with outputs_to_working_directory: false
on 23.0 and the last stable version of pulsar ? I think the tests should now be failing if this was still a problem. Feel free to re-open if it isn't fixed.
On some (but not all) pulsar deployments, we found a bug in the creation of the
html.files_path
directory while running Alphafold jobs on pulsar. Pulsar returns an incorrect value forhtml.files_path
which includes a second working directory level i.e.working/working
.Context
The issue only surfaces when the HTML output makes a request for static assets (PDB files) from the
html.files_path
. The HTML webpage requests these files with a relative URL (e.g.ranked_0.pdb
) but the job directory structure is not what the server expects. Therefore, it fails to locate the file and returns a 404.Details
I believe that our pulsar job directory should look something like:
But
html.files_path
is created inside an additionalworking
dir:Suggestions
When creating the
html.files_path
, perhaps the interpreter is assumed to be in the job directory but is in fact in the working directory, thereby creating a second childworking
directory when rendering this path.Our hacky fix for this issue is this final line in the tool
<command>
section to correct thehtml.files_path
location, if the bug has occurred: