Open waoverholt opened 4 years ago
I've been having the same issue. Let me know if you found a solution
I had the same issue after manually installing the database (v10). I could solve it by creating a folder within the enrichm_database_v10 folder called '26-11-2018' and copying the VERSION file into this new folder. To my surprise - it worked! enrichM is happily running.
Hi DennyPopp, Could you share how you manually installing the database and setup. thanks.
I installed enrichm using pip and have
Version: 0.6.3
For what I have done, I do download the v10 and uncompress it here
~/bio_db/enrichm_db/
now set env path
ENRICHM_DB=~/bio_db/enrichm_db/enrichm_database_v10
I creati a folder within the enrichm_database_v10 folder called '26-11-2018' and copying the VERSION file into this new folder. but still error
any ideas
Traceback (most recent call last):
File "/usr/local/bin/enrichm", line 352, in <module>
run.run_enrichm(args, sys.argv)
File "/usr/local/lib/python3.8/dist-packages/enrichm/run.py", line 409, in run_enrichm
pipeline(args)
File "/usr/local/lib/python3.8/dist-packages/enrichm/run.py", line 282, in run_annotate
annotate = Annotate(# Define inputs and outputs
File "/usr/local/lib/python3.8/dist-packages/enrichm/annotate.py", line 113, in __init__
self.databases = Databases()
File "/usr/local/lib/python3.8/dist-packages/enrichm/databases.py", line 71, in __init__
raise Exception(f"\nNo database version file found. Have you: \n\
Exception:
No database version file found. Have you:
- Installed the EnrichM database using the 'enrichm data' command?
- Specified the location of the EnrichM database by exporting a bash variable called ENRICHM_DB? (Currently I'm looking here: /home/dell/bio_db/enrichm_db/enrichm_database_v10)
Hello,
I've been trying to install EnrichM and I keep running into the same problem (tried with 2 versions of python, 3.6 & 3.8).
When I try running
enrichm data --output /path/
I get the following errorI tried to get around that by manually installing and unpacking the latest database version (v10). When I point ENRICHM_DB to the unpacked tarball I get this error:
The first issue seems to be a urllib error, and I saw somewhere online that changing the import statement from
import urllib
to importurllib.request as urllib
might fix it, but I haven't tried this modification yet.The database error is clearly an issue with the path specification since the file VERSION within enrichm_database_v10 points to 26-11-2018 Probably because I haven't formatted something correctly that the
enrichm data1
does.To install enrichM I've tried:
I also forced it to try using python3.8:
About my environment:
Thanks for your time!
Best, Will