combogenomics / DuctApe

Analyze and link genomics and phenomics experiments
http://combogenomics.github.io/DuctApe
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sqlite3 database not supported #11

Open geboro opened 1 week ago

geboro commented 1 week ago

Hello.

I am trying DuctApe with the tutorial dataset (smeliloti), and I couldn't pass the first step, since dape init failed to create the sqlite3 database

I'm using a xubuntu 22.04.4 LTS OS running on a Xeon Gold 6140 system, and I followed the installation instructions with conda (mamba) as per the tutorial.

Thanks!

$ dape init -n smeliloti
10:22:52 - Could not create the database!
10:22:52 - database is locked
10:22:52 - You can remove or rename the old project file
Traceback (most recent call last):
  File "/home/bioinf/miniforge3/envs/ductape/bin/dape", line 1015, in <module>
    touchProject(project)
  File "/home/bioinf/miniforge3/envs/ductape/lib/python3.12/site-packages/ductape/actions.py", line 4832, in touchProject
    proj = Project(project)
           ^^^^^^^^^^^^^^^^
  File "/home/bioinf/miniforge3/envs/ductape/lib/python3.12/site-packages/ductape/storage/SQLite/database.py", line 126, in __init__
    self.getProject()
  File "/home/bioinf/miniforge3/envs/ductape/lib/python3.12/site-packages/ductape/storage/SQLite/database.py", line 154, in getProject
    cursor = conn.execute('select * from project limit 1;')
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
sqlite3.OperationalError: no such table: project
mgalardini commented 6 days ago

Hi, I'm afraid DuctApe is not maintained much anymore. I might find some time to look at this but I cannot really make any commitment, sorry