WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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DRAM-setup.py broke when upgrading to v1.5.0 #326

Closed ChristopherBurgess-USDA closed 8 months ago

ChristopherBurgess-USDA commented 8 months ago

I can't seem to get DRAM-setup.py to work after upgrading to the newest DRAM version.

❯ DRAM-setup.py -h
  File "/home/christopher.burgess/.conda/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?

I've tried completely uninstalling the environment and cleaning my conda cache with no luck. Is this a problem on my end or was there a bug in the release?

ChristopherBurgess-USDA commented 8 months ago

Quick update, I took a peak at DRAM-setup.py and there is definately a syntax error there on line 122 (below). It looks like the camper argument help was pasted in the wrong spot.

    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')

Here is the fixed code:

    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')
smdabdoub commented 8 months ago

This was fixed in commit 9ff00c9