Software installed (and commands run) specific for the Durban 2018 Workshop.
- Manually installed QIIME2 version 2018.6 as ansible script not working. Followed instructions here.
wget https://data.qiime2.org/distro/core/qiime2-2018.6-py35-linux-conda.yml
conda env create -n qiime2-2018.6 --file qiime2-2018.6-py35-linux-conda.yml
- quant3p installed via python following instructions here. Need to be sudo to do this. This also installed macs2 and macs2-stranded as part of the dependency installation.
sudo python setup.py install
- STAR downloaded from github here and compiled from source and copied to bin as su master.
wget https://github.com/alexdobin/STAR/archive/2.6.0a.tar.gz
tar -xzf 2.6.0a.tar.gz
cd STAR-2.6.0a/source
make STAR
sudo cp ./STAR /usr/local/bin
- GSEA downloaded from here. The GUI is launched directly from the website and is also available as an icon on the desktop. Downloaded the command line jar file and saved in ~/software. This is launched as follows:
java -jar /home/genomics/software/gsea-3.0.jar
- Additional R packages installed as follows:
install.packages("tidyverse")
source("http://www.bioconductor.org/biocLite.R")
biocLite("microbiome")
install.packages("ggpubr")
install.packages("UpSetR")
source("https://bioconductor.org/biocLite.R")
biocLite("ggtree")
devtools::install_github("benjjneb/dada2")
install.packages("pheatmap")
install.packages("ggdendro")
-
Manually updated the desktop background image
-
Changed timezone for Durban as follows:
sudo timedatectl set-timezone Africa/Johannesburg
- BBTools downloaded from SourceForge here, unpackaged and copied all scripts to bin as su master.
wget https://sourceforge.net/projects/bbmap/files/BBMap_38.23.tar.gz
tar -xzvf BBMAP_38.23.tar.gz
sudo cp -r ./bbmap/* /usr/local/bin
- MetaPhlAn2 installed via bioconda
conda install metaphlan2 -c bioconda