galaxyproject / galaxyproject/galaxy

run_tool_shed.sh error

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Description

Hello,

I have Galaxy (release_19.05) installed and running well on Debian 10 (Buster) with Python2.7. However, when I try to run `sh run_tool_shed.sh` to have a local Tool Shed, at some point I got the error below.

For information, I got the exactly same behaviour with Python3 (Galaxy runs well and got the same error when I try to start local Tool Shed).

Thank you for your help,
Joan

```
galaxy.datatypes.registry DEBUG 2019-09-10 16:34:33,772 [p:962,w:0,m:0] [MainThread] No build sites source located.
Traceback (most recent call last):
File "lib/galaxy/webapps/tool_shed/buildapp.py", line 69, in app_factory
app = UniverseApplication(global_conf=global_conf, **kwargs)
File "lib/galaxy/webapps/tool_shed/app.py", line 47, in __init__
from galaxy.webapps.tool_shed.model.migrate.check import create_or_verify_database
File "lib/galaxy/webapps/tool_shed/model/migrate/check.py", line 13, in
migrate_repository = repository.Repository(migrate_repository_directory)
File "/galaxy/.venv/local/lib/python2.7/site-packages/migrate/versioning/repository.py", line 77, in __init__
self.verify(path)
File "/galaxy/.venv/local/lib/python2.7/site-packages/migrate/versioning/repository.py", line 98, in verify
raise exceptions.InvalidRepositoryError(path)
InvalidRepositoryError: libwebapps/tool_shed/model/migrate
```

Contributor guide

Open the contributing guide

Research direction

Start by reading run_tool_shed.sh, lib/galaxy/webapps/tool_shed/buildapp.py, and lib/galaxy/webapps/tool_shed/model/migrate/check.py, then trace the migration repository path reported in the traceback. Done means the local Tool Shed starts without InvalidRepositoryError.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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