Working environment¶

The working environment will already contain everything you need to get started. If specific files are required, we will download them during the exercises.

The used system¶

Here is some information on the system we have been using. This is important because some of the installation commands given here are specific for this version of Ubuntu:

$ cat /etc/os-release
NAME="Ubuntu"
VERSION="18.04.1 LTS (Bionic Beaver)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 18.04.1 LTS"
VERSION_ID="18.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=bionic
UBUNTU_CODENAME=bionic

Changes to the environment¶

We use several bash aliases to mask complex docker commands which we added globally to /etc/bash.bashrc. This file is available here. If you would like to use these settings locally, you can add these lines to your own .bashrc file (or equivalent).

# a few aliases of docker run commmands
alias pandoc='docker run --rm -it -v `pwd`:/data -w /data reslp/pandoc:3.7.0.2 pandoc'
alias debian-alternative-miniconda='docker run --rm -it -v `pwd`:/data reslp/debian-alternative-miniconda:4.7.12'
alias nextflow='docker run --rm -it -v `pwd`:/data -w /data nextflow/nextflow:22.04.4 nextflow '
alias nf-core='docker run -it -v `pwd`:`pwd` -w `pwd` -u $(id -u):$(id -g) nfcore/tools:2.4.1'
alias switch-on_ubuntu_20-04="docker run -it --rm --hostname ubuntu-20-04 -w /home ubuntu:20.04"
alias switch-on_ubuntu_22-04="docker run -it --rm --hostname ubuntu-22-04 -w /home ubuntu:22.04"

Docker installation¶

This is how we installed Docker. This is based on these instructions.

$ sudo apt update
$ sudo apt install apt-transport-https ca-certificates curl software-properties-common
$ curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
$ sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu bionic stable"
$ sudo apt update
$ sudo apt install docker-ce
$ sudo systemctl status docker
$ sudo usermod -aG docker ${USER} #add current user to docker group
$ su - ${USER} #password required - alternatively log off and back on to activate
$ #check if user is part of docker group
$ id -nG

Singularity installation¶

This is how we installed Singularity, originally given in the Github issue thread here (way down in the thread).

$ sudo apt-get update && \
  sudo apt-get install -y build-essential \
$ libseccomp-dev pkg-config squashfs-tools cryptsetup

$ sudo rm -r /usr/local/go

$ export VERSION=1.13.15 OS=linux ARCH=amd64  # change this as you need

$ wget -O /tmp/go${VERSION}.${OS}-${ARCH}.tar.gz https://dl.google.com/go/go${VERSION}.${OS}-${ARCH}.tar.gz && \
  sudo tar -C /usr/local -xzf /tmp/go${VERSION}.${OS}-${ARCH}.tar.gz

$ echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \
  echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \
  source ~/.bashrc

$ curl -sfL https://install.goreleaser.com/github.com/golangci/golangci-lint.sh |
  sh -s -- -b $(go env GOPATH)/bin v1.21.0

$ mkdir -p ${GOPATH}/src/github.com/sylabs && \
  cd ${GOPATH}/src/github.com/sylabs && \
  git clone https://github.com/sylabs/singularity.git && \
  cd singularity

$ git checkout v3.6.3

$ cd ${GOPATH}/src/github.com/sylabs/singularity && \
  ./mconfig && \
  cd ./builddir && \
  make && \
  sudo make install

$ singularity version

The conda setup¶

We are using Miniconda3 v4.8.2 installed globally, like so:

$ cd ~
$ mkdir conda
$ cd conda
$ wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh
$ bash ./Miniconda3-py37_4.8.2-Linux-x86_64.sh
$ #basedir: /home/ubuntu/conda/miniconda3
$ #conda init -> yes
$ . ~/.bashrc
$ conda config --set auto_activate_base false

Here is some additional information on the exact configuration as we have it on the server:

$ conda --version
conda 4.8.2
$ conda info
conda info

     active environment : None
            shell level : 0
       user config file : /home/ubuntu/.condarc
 populated config files : /home/ubuntu/.condarc
          conda version : 4.8.2
    conda-build version : not installed
         python version : 3.7.6.final.0
       virtual packages : __glibc=2.27
       base environment : /home/ubuntu/conda/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/ubuntu/conda/miniconda3/pkgs
                          /home/ubuntu/.conda/pkgs
       envs directories : /home/ubuntu/conda/miniconda3/envs
                          /home/ubuntu/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.6 Linux/5.4.0-1080-aws ubuntu/16.04.5 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False
$ cat /home/ubuntu/.condarc
channels:
  - conda-forge
  - bioconda
  - defaults
auto_activate_base: false

Already created conda environments¶

You should have a conda environment available that we created called serpentesmake which we will be using in the exercise on Snakemake. In case it is not available you can get the YAML file here.