Installation
Download the WebAtlas Pipeline release. You can look for previous releases on GitHub.
Using wget
wget https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.5.2.tar.gz
Resolving github.com (github.com)... 140.82.121.3
Connecting to github.com (github.com)|140.82.121.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.5.2 [following]
--2023-05-18 09:30:15-- https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.5.2
Resolving codeload.github.com (codeload.github.com)... 140.82.121.9
Connecting to codeload.github.com (codeload.github.com)|140.82.121.9|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/x-gzip]
Saving to: ‘v0.5.2.tar.gz’
v0.5.2.tar.gz [ <=> ] 2.70M 9.12MB/s in 0.3s
2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.5.2.tar.gz’ saved [2835534]
Using curl
curl -L -o v0.5.2.tar.gz https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.5.2.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2844k 0 2844k 0 0 1970k 0 --:--:-- 0:00:01 --:--:-- 2539k
Extract the WebAtlas compressed tag and change directory into the new repo.
tar -xzvf ./v0.5.2.tar.gz
cd webatlas-pipeline-0.5.2
webatlas-pipeline-0.5.2/
webatlas-pipeline-0.5.2/.github/
...
...
webatlas-pipeline-0.5.2/tests/input/simple_config.json
webatlas-pipeline-0.5.2/tests/test_class.py
Environment setup
Follow these Environment Setup instructions using conda or manually installing the required components to run WebAtlas.
If you have conda or mamba already installed then you can use the environment.yaml file included in the WebAtlas release to create the environment.
conda env create -f envs/environment.yaml
Then make sure you activate the webatlas environment before you use the pipeline.
conda activate webatlas
Warning
Users working on newer Silicon-based Macs may encounter problems installing this environment. Some packages have not yet been compiled for Apple silicon processors therefore, we recommend you install the packages originally compiled for Mac computers with Intel processors. Set an environment variable that specifies the architecture before installing and activating the Conda environment, like this:
export CONDA_SUBDIR=osx-64
conda env create -f envs/environment.yaml
conda activate webatlas
#1. Check git is installed
Make sure git 2.17 or later is installed on your computer by using the command:
git --version
git version 2.25.1
If Git is missing you will have to follow the Getting Started Installing Git guide.
#2. Install Nextflow
Java is required by Nextflow. Refer to Nextflow’s guidelines to install it.
Enter the following command in your terminal to install Nextflow in the current directory:
Using wget
wget -qO- https://get.nextflow.io | bash
Using curl
curl -s https://get.nextflow.io | bash
CAPSULE: Downloading dependency org.apache.ivy:ivy:jar:2.5.1
...
CAPSULE: Downloading dependency io.nextflow:nf-commons:jar:23.04.1
N E X T F L O W
version 23.04.1 build 5866
created 15-04-2023 06:51 UTC (07:51 BST)
cite doi:10.1038/nbt.3820
http://nextflow.io
Nextflow installation completed. Please note:
- the executable file `nextflow` has been created in the folder: ./webatlas-pipeline
- you may complete the installation by moving it to a directory in your $PATH
You can read more about how to install nextflow in the official nextflow documentation.
#3. Check Docker is installed (optional)
If you want to use Docker, make sure Docker Engine 20.10 or later is installed on your computer by using the command:
docker version
Client: Docker Engine - Community
Version: 23.0.4
API version: 1.42
Go version: go1.19.8
Git commit: f480fb1
Built: Fri Apr 14 10:32:23 2023
OS/Arch: linux/amd64
Context: default
Follow the official Docker Install guide if it is not installed already.