Issue with conda install of bgwas3

[rarichards]

conda install -c g-r-eg bgwas3

bgwas3 make full


Returns:

pkg_resources.DistributionNotFound: The 'bgwas3==1.0' distribution was not found and is required by the application

I'm not sure what caused it. Potentially an issue with the OS installation of Python or the conda package. This was resolved with a manual installation with Python 3.8:

1. conda create -n bgwas3 python=3.8
2. Install dependencies.
3. Install bgwas3:
   
   git clone https://github.com/gregoryleeman/bgwas3.git

cd bgwas3

pip install .

cd ..

bgwas3 --help

[rarichards]

Installing bgwas3 like this doesn't correctly install all files.

bgwas3 make full failed, see exception 1 in pipeline1.log:
Exception #1 \ 'builtins.OSError(--------------------------------------- \ Child was terminated by signal -2: \ The stderr was: \ \ Rscript /home/ruth/miniconda3/envs/bgwas3/lib/python3.8/site-packages/bgwas3/R/split_phenos.R phenos.tsv phenos \

Rscript /home/ruth/miniconda3/envs/bgwas3/lib/python3.8/site-packages/bgwas3/R/split_phenos.R phenos.tsv phenos did not exist because /home/ruth/miniconda3/envs/bgwas3/lib/python3.8/site-packages/bgwas3/R/ had not installed properly, nor had directories plots and python. Manually copying these three directories into the bgwas3 directory fixed it.

[rarichards]

Potential issue with prokka installation.

I ran into problems trying to run the annotate step, with the following error: Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module). I tried a number of fixes but the only way I could get it to work was with a fresh install of bgwas3, AFTER a fresh install of prokka.

create env:

conda create -n bgwas3 python=3.7
conda activate bgwas3

install bgwas3:

git clone https://github.com/gregoryleeman/bgwas3.git
cd bgwas3  
pip install .  
cd ..

install prokka according to bioconda/bioconda-recipes#10277:

conda install -c bioconda prokka=1.13 minced=0.3.0 parallel=20180522

install the remaining dependencies:

conda install cgatcore
conda install r-argparse r-dplyr r-readr r-tidyr r-stringr r-ggplot2 r-tidytree
conda install mako
pip install argparse # conda doesn't seem to have a recipe for argparse for python 3.8
conda install pandas dendropy
conda install fsm-lite roary mash

check installation:

prokka -h
bgwas3 -h

with this method, bgwas3/plots/, bgwas3/python/, bgwas3/R/ aren't installed and need to be manually copied over (see my previous comment).