Closed erinyoung closed 4 years ago
Hi, Just wanted to say I noticed the same issue with porechop. Your fix didn't do the trick for me though. I ended up using the manual python3 install, which worked:
git clone https://github.com/artic-network/Porechop.git
cd Porechop
python3 setup.py install
In the end I discovered that the pipeline doesn't use porechop anymore (my consensus sequences are identical with / without porechop in my PATH). The pipeline now uses Guppy barcoder for demuxing. So I guess this issue is not relevant any more.
I just looked at some of their updates, and it looks like they aren't using porechop anymore. Closing the issue.
My default gcc for my OS is 4.8.5. This matters because when I went to use the yaml to create the conda environment for the artic protocol, artic's version of porechop did not install. I didn't realize that 1) artic was using their specific version of porechop, and 2) that it didn't install because there was no error message.
When I went to install artic's version of porechop in the environment, I came across this error:
error: [Errno 2] No such file or directory: 'porechop/cpp_functions.so'
I now knew that it was a compiling issue (needs >gcc 5) and added this to my environment:
Additionally, I realized that bcftools=1.9 and seqtk=1.3 didn't install in the conda environment either. I didn't realize this until after I went through each dependency after I realized the porechop issue.
It'd be helpful if there was a version check for each required package.