Running SymPortal

Create the env as a python 3.6 environment

conda create -n symportal_python python=3.6

Activate the environment (it can be deactivated with ‘conda deactivate’)

conda activate symportal_python

Use GitHub to download latest version

git clone https://github.com/didillysquat/SymPortal_framework.git cd SymPortal_framework

Then install the remaining python packages

python3 -m pip install numpy==1.17.1 python3 -m pip install biopython==1.71 python3 -m pip install Django==2.2.4 python3 -m pip install matplotlib==2.0.2 python3 -m pip install -r requirements.txt

Install other dependencies

conda install mothur==1.39.5 (needs version 1.39.5) conda install mafft conda install iqtree

Then follow steps 2a, 2b, and 4 from here:

[SymPortal]https://github.com/didillysquat/SymPortal_framework/wiki/SymPortal-setup

Test

which mothur ~/miniconda3/envs/symportal_python/bin/mothur

which blastn /usr/local/bin/blastn

which makeblastdb /usr/local/bin/makeblastdb

which mafft ~/miniconda3/envs/symportal_python/bin/mafft

which iqtree ~/miniconda3/envs/symportal_python/bin/iqtree

blastn -version blastn: 2.2.31+ Package: blast 2.2.31, build Jun 12 2018 14:50:12

makeblastdb -version makeblastdb: 2.2.31+ Package: blast 2.2.31, build Jun 12 2018 14:50:12

mafft –version v7.455 (2019/Dec/7)

Running on the 14 HoloInt Test samples

HoloInt ITS2 Sample Preparation

Activate Program

conda activate symportal_python

Load Data

./main.py –load ../ITS2/ –name first_loading –num_proc 3 –data_sheet /home/hputnam/Sym/SymPortal_datasheet_20191223.xlsx

Running Analysis

./main.py –analyse 1 –name first_analysis –num_proc 3