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DRAM-setup.py in v1.5.0 has invalid syntax #360

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donovan-parks opened this issue Sep 25, 2024 · 1 comment
Open

DRAM-setup.py in v1.5.0 has invalid syntax #360

donovan-parks opened this issue Sep 25, 2024 · 1 comment

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@donovan-parks
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Hi. I am installing DRAM onto a fresh Ubuntu VM via mamba. Installation into a conda environment works without issue. However, setting up of the DRAM DBs with DRAM-setup.py is currently broken::

>DRAM-setup.py -h
  File "/home/dparks/miniforge3/envs/DRAM/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?

This does indeed appear to be due to invalid syntax on line 124 of DRAM-setup.py as shown below:

    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')
    set_db_locs_parser.add_argument('--peptidase_loc', default=None,
                                    help='mmseqs2 database file from MEROPS database')

Cheers,
Donovan

@Gsmith535
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Gsmith535 commented Dec 20, 2024

As devs have mentioned elsewhere, the best solution is to wait for DRAM v2.

This is probably the best way to fix, but not necessarily encouraged by devs:
#330

Edited to replace hack-ey solution with better one.

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