Closed evolarjun closed 3 years ago
jeanrjc
commented
3 years ago You can try to install like this instead :
conda create --name IFv2 python=3.6
conda config --add channels bioconda # if it's not already the case
conda activate IFv2
conda install integron_finder # install integron_finder
conda install biopython==1.72 # downgrade biopython and pandas waiting for upcoming fixes
conda install pandas=0.25.3
integron_finder ...
conda deactivate@bneron wasn't it fix ?
evolarjun
commented
3 years ago I gave up on conda and the release version, and was able to get the master branch on git working using the following on an Ubuntu 20.04 box. My end goal was an installation for multiple users, so this worked well:
# prerequisites
# hmmer
sudo apt-get install hmmer
# prodigal
mkdir prodigal
cd prodigal
wget https://github.com/hyattpd/Prodigal/releases/download/v2.6.3/prodigal.linux
chmod 755 prodigal.linux
sudo mv prodigal.linux /usr/local/bin/prodigal
cd ..
rmdir prodigal
# nextflow
# (requires Java)
sudo apt-get install default-jre
java --version
# nextflow
curl -s https://get.nextflow.io | bash
sudo mv nextflow /usr/local/bin
sudo chmod a+r /usr/local/bin/nextflow
# now install integron_finder
sudo apt-get install python3-pip
git clone https://github.com/gem-pasteur/Integron_Finder.git
cd Integron_Finder
sudo python3 -m pip install --system -e .I will try the conda instructions you posted above and report back.
evolarjun
commented
3 years ago I just tried the bioconda instructions above and they appear to work too.
Thanks!
joshamilton
commented
2 years ago As of September 23, 2021, the colorlog package also needs to be downgraded to prevent the error message:
Traceback (most recent call last): File "/home/ec2-user/anaconda3/envs/integron_finder/bin/integron_finder", line 10, in
sys.exit(main()) File "/home/ec2-user/anaconda3/envs/integron_finder/lib/python3.6/site-packages/integron_finder/scripts/finder.py", line 513, in main out=not config.mute) File "/home/ec2-user/anaconda3/envs/integron_finder/lib/python3.6/site-packages/integron_finder/init.py", line 78, in init_logger logging = colorlog.logging.logging AttributeError: module 'colorlog' has no attribute 'logging'
Downgrading to 4.8.0 allows integron_finder to run. I did not try intermediate versions between 4.8.0 and the current 6.4.1.
bneron
commented
2 years ago or use the master version of Integron_Finder
Problem installing integron_finder via bioconda:
Version of Integron_Finder:
Write here the output of integron_finder --version. No output.
OS
Expected behavior
Get version. Note:
Actual behavior
Steps to reproduce behavior
See above
Relevant logs and/or screenshots
(Paste any relevant logs - please use code blocks (```) to format console output, logs, and code as it's very hard to read otherwise.)