`planemo shed_update` updates suites before contained tools

[nsoranzo]

Noticed when adding a tool to suite_samtools in https://github.com/galaxyproject/tools-iuc/pull/3740 .

[eschen42]

@nsoranzo I hit this this issue which may be a duplicate of issue 1194

The pertinent file is .shed.yml linked here and the error message that appears, notwithstanding the fact that I have no repository_dependencies.xml, is

(venv) rstudio@a969faad142e:~/src/mqppep_smoke/mqppep/tools/mqppep$ planemo shed_upload --owner eschen42 -t local .
cd '/home/rstudio/src/mqppep_smoke/mqppep/tools/mqppep' && git rev-parse HEAD
galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
git diff --quiet
Could not update mqppep_preproc
('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
cd '/home/rstudio/src/mqppep_smoke/mqppep/tools/mqppep' && git rev-parse HEAD
galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
git diff --quiet
Could not update mqppep_anova
('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))
cd '/home/rstudio/src/mqppep_smoke/mqppep/tools/mqppep' && git rev-parse HEAD
galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
git diff --quiet
Could not update suite_mqppep
Unexpected HTTP status code: 500: {"err_msg": "The repository_dependencies.xml file contains an invalid <repository> tag.  Invalid latest installable changeset_revision 000000000000 retrieved for repository mqppep_preproc owned by eschen42.  "}

[ebolyen]

I'm having this issue as well. My solution has been to go back to the broken repositories and upload a single file. I hope this is something that can get fixed in the future, as it makes auto_tool_repositories very difficult to use as far as I can tell.