BaseAppConfiguration.root is now an absolute path, and so is
BaseAppConfiguration.data_dir, so the result of
`resolve_path(kwargs.get("tool_dependency_dir", "dependencies"), self.data_dir)`
is not "none" as it used to be, but `"<galaxy_data_dir>/none"` and so
the fallback will not be used.
This can be fixed by setting the default target dir to `dependencies`
and join it to self.data_dir, which defaults to `galaxy_root/database`
on classic installations.
Fixes the issues in https://github.com/galaxyproject/galaxy/pull/8195#issuecomment-513246346
uwsgi options are returned as bytestring, so this avoids:
```
Traceback (most recent call last):
File "lib/galaxy/webapps/galaxy/buildapp.py", line 12, in <module>
import galaxy.app
File "lib/galaxy/app.py", line 8, in <module>
import galaxy.model
File "lib/galaxy/model/__init__.py", line 45, in <module>
import galaxy.exceptions
File "lib/galaxy/exceptions/__init__.py", line 19, in <module>
from ..exceptions import error_codes
File "lib/galaxy/exceptions/error_codes.py", line 9, in <module>
from galaxy.util import unicodify
File "lib/galaxy/util/__init__.py", line 1708, in <module>
executable = _executable()
File "lib/galaxy/util/__init__.py", line 1700, in _executable
exe = os.path.join(virtualenv, 'bin', 'python')
File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.6/posixpath.py", line 94, in join
genericpath._check_arg_types('join', a, *p)
File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.6/genericpath.py", line 151, in _check_arg_types
raise TypeError("Can't mix strings and bytes in path components") from None
TypeError: Can't mix strings and bytes in path components
```
Broken in https://github.com/galaxyproject/galaxy/commit/891daf4f82eb45c692f3fc5542cea35f94e10118
When a fastq file contains quality scores that are too low to be
compatible with any +64 encoding scheme, the assumption should be
that the file is Phred+33 encoded even if some scores are above
the current upper threshold of 44.
instance_id is a string, so this can't be compared to an integer
on python 3. Broken in ac1b25ed4c,
prior to that the comparison was `len(self._galaxy_instance_id) > 0:`
instance_id is a string, so this can't be compared to an integer
on python 3. Broken in ac1b25ed4c,
prior to that the comparison was `len(self._galaxy_instance_id) > 0:`
Daniel Blankenberg