Team3-FunctionalAnnotation/Environment_Instructions at master · compgenomics2020/Team3-FunctionalAnnotation · GitHub

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######## Setting up the enviroment documentation ########

#go to the path where miniconda is to be added and export it to the $PATH vairble in your .bashrc

### the following steps are to install miniconda and only one person needs to do it


wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh

bash Miniconda2-latest-Linux-x86_64.sh

conda create T3FN

###########For other users##########

#add the location of export PATH="/home/projects/group-c/Team3-GenePrediction/usr/miniconda/bin:$PATH in .bashrc

conda init
conda activate T3FN

#you can install new tools using conda install toolname or look up conda documentation for the exact code needed.

##########Setting up the Conda T3FN for Genome Assembly#############
#blast v2.9.0
conda install -c bioconda blast
#rgi v5.1.0
conda install -c bioconda rgi
#r-rbokeh v0.6.3
conda install -c anaconda r-rbokeh
#elfutils v0.176
conda install -c conda-forge elfutils
#java v11.0.1
conda install -c conda-forge openjdk
#bedtools 2.29.2
conda install -c bioconda bedtools
#eggNOG-mapper v2.0.1
conda install -c bioconda eggnog-mapper
#prokka v1.14.6
conda install -c bioconda prokka
#emboss v6.6.0
conda install -c bionconda emboss