DRAM-setup.py contains syntax error in v1.5.0 (missing comma / broken argument definition)

[fengwangjue-gif]

Description of the bug

While installing DRAM (DRAM-bio==1.5.0) in a fresh conda environment (Python 3.10), DRAM.py installs successfully, but DRAM-setup.py fails immediately with a SyntaxError.
The error occurs before any database configuration is attempted.

Error Message
File ".../envs/dram_env/bin/DRAM-setup.py", line 124
set_db_locs_parser.add_argument('--camper_tar_gz_loc', default=None,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
SyntaxError: invalid syntax. Perhaps you forgot a comma?

Problematic Code Snippet
Lines 123–127 in the installed DRAM-setup.py look like this:
set_db_locs_parser.add_argument('--viral_loc', default=None,
set_db_locs_parser.add_argument('--camper_tar_gz_loc', default=None,
help='The source for the CAMPER database files, this is a tar.gz file downloaded'
' from the release page https://github.com/WrightonLabCSU/CAMPER/releases')
help='mmseqs2 database file from ref seq viral gene collection')

The --viral_loc argument appears to be truncated and missing its help= definition, causing a syntax error.

Correct structure should be something like:
set_db_locs_parser.add_argument('--viral_loc', default=None,
help='mmseqs2 database file from ref seq viral gene collection')
set_db_locs_parser.add_argument('--camper_tar_gz_loc', default=None,
help='The source for the CAMPER database files, this is a tar.gz file downloaded'
' from the release page https://github.com/WrightonLabCSU/CAMPER/releases')

System information

DRAM-bio version: 1.5.0
Installed via: pip (inside conda environment)
Python version: 3.10
OS: Linux (HPC cluster)

Command used and terminal output

Relevant files

No response

[madeline-scyphers]

It seems like that already got fixed in DRAM-setup.py awhile back, but wasn't released. You could install directly from master if you are trying to use DRAM1. We aren't supporting DRAM1 or developing on it anymore, and at the moment we don't have it setup to release to DRAM1 at all. I would suggest either installing directly with pip from from the github url, or installing DRAM2, or waiting for the DRAM2 release. We are doing our full DRAM2 release in the summer.

[fengwangjue-gif]

Thank you very much for the clarification and for the update.That makes sense — I’ll work with the GitHub source version for now and also keep an eye on DRAM2.Really appreciate your help!