Entering edit mode
3.5 years ago
pavelasquezv
▴
50
Hi all,
I am running a program from the REPET program
TEdenovo.py -P DmelChr4 -C TEdenovo.cfg -S 1
and I get the following error:
File "/media/hd2/pedrovasconez/TEtranscripts/REPET_linux-x64-3.0/bin/TEdenovo.py", line 53, in <module>
from commons.core.LoggerFactory import LoggerFactory
ImportError: No module named commons.core.LoggerFactory
Please, it would be highly appreciated if someone could help me to resolve this error.
Thanks a lot
Alex
The
pythonmodules are located inREPET_linux-x64-3.0/commonsfolder, include the installation directory inPYTHONPATH. The best solution will be to create a virtual environment.Thanks for your reply my friend. I ran the following command but the same error still persists.
export PYTHONPATH=$PYTHONPATH:/media/hd2/pedrovasconez/TEtranscripts/REPET_linux-x64-3.0TEdenovo.py: command not found.
Many thanks for your time
All the best
Hard to tell, best guess would be to install that module. Is this a published script you use? If so, does it contain a manual with dependencies to install first? Please give a link to the tool/script.
Hi, many thanks for your reply. This is a tutorial on the REPET program.
https://urgi.versailles.inra.fr/Tools/REPET/TEdenovo-tuto
It is a program for the annotation of transposition elements. Please, I would be very happy if you told me how to install the dependencies of this program if they exist. I am new to bioinformatics.
Thanks a lot again,
Alex
Here is an INSTALL section, try to go through it, if you need help please say where exactly: https://urgi.versailles.inra.fr/Tools/REPET/INSTALL
Thank you for your cooperation. I am currently unable to download the Repbase database. https://www.girinst.org/server/RepBase/index.php Please, if you have any suggestions, I would appreciate it if you would let me know.