cbielow

> if (!require(devtools, quietly = TRUE)) install.packages("devtools")
Installing package into ‘C:/Users/cbielow/AppData/Local/Temp/RtmpcVFTaT/PTXQC_pck_179824f171d4’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
also installing the dependencies ‘curl’, ‘memoise’, ‘whisker’, ‘evaluate’, ‘digest’, ‘rstudioapi’, ‘jsonlite’, ‘roxygen2’, ‘rversions’, ‘git2r’

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.1/curl_0.9.3.zip'
Content type 'application/zip' length 4384766 bytes (4.2 Mb)
opened URL
downloaded 4.2 Mb

cbielow

## manually install contrib libs: SEQAN,COINOR,WILDMAGIC,(KISSFFT)
##manually: install miniconda3

conda create --name oms python
conda install -n oms xerces-c=3.2.0
conda install -n oms boost=1.65.1
conda install -n oms eigen
conda install -n oms cmake

source activate oms

cbielow

This guide will show you how to install conda and then use it to install nextflow and singularity for executing popular bioinformatics workflows. Unfortunately, singularity is not available on Windows or macOS. So, this guide will only target Linux environments. If you have to use Windows 10, then try WSL2. If you have to use macOS, then try a Virtual Machine.

Download the Miniconda3 installer for Linux environments:

curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh

Install into a folder named miniconda3 under your home directory, and delete the installer:

bash miniconda.sh -bup $HOME/miniconda3 && rm -f miniconda.sh